Package List¶
This is a list of things you can install using Spack. It is automatically generated based on the packages in the latest Spack release.
Spack currently has 2429 mainline packages:
abinit¶
- Homepage:
- Spack package:
- Versions:
- 8.6.3, 8.2.2, 8.0.8b
- Build Dependencies:
- libxc, fftw, mpi, lapack, scalapack, blas, hdf5, netcdf-fortran
- Link Dependencies:
- libxc, fftw, mpi, lapack, scalapack, blas, hdf5, netcdf-fortran
- Description:
- ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time- Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.
abyss¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2, 1.5.2
- Build Dependencies:
- sparsehash, boost, sqlite, mpi, automake, autoconf, libtool
- Link Dependencies:
- sparsehash, libtool, boost, sqlite, mpi
- Description:
- ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.
ack¶
- Homepage:
- Spack package:
- Versions:
- 2.22, 2.18, 2.16, 2.14
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Description:
- ack 2.14 is a tool like grep, optimized for programmers. Designed for programmers with large heterogeneous trees of source code, ack is written purely in portable Perl 5 and takes advantage of the power of Perl's regular expressions.
activeharmony¶
- Homepage:
- Spack package:
- Versions:
- 4.5
- Description:
- Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).
adept-utils¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0
- Build Dependencies:
- cmake, boost, mpi
- Link Dependencies:
- boost, mpi
- Description:
- Utility libraries for LLNL performance tools.
adios¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
- Build Dependencies:
- netcdf, hdf5, zlib, libtool, automake, mpi, autoconf, szip, lz4, m4, bzip2, dataspaces, libevpath, zfp, python, c-blosc, sz
- Link Dependencies:
- netcdf, hdf5, zlib, bzip2, szip, lz4, c-blosc, dataspaces, libevpath, zfp, mpi, sz
- Description:
- The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
adios2¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.0.0
- Build Dependencies:
- py-numpy, zeromq, hdf5, adios, cmake, bzip2, py-mpi4py, python, mpi, zfp
- Link Dependencies:
- zeromq, hdf5, bzip2, adios, python, mpi, zfp
- Run Dependencies:
- py-numpy, python, py-mpi4py
- Description:
- Next generation of ADIOS developed in the Exascale Computing Program
adlbx¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0
- Build Dependencies:
- exmcutils, mpi
- Link Dependencies:
- exmcutils, mpi
- Description:
- ADLB/X: Master-worker library + work stealing and data dependencies
adol-c¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.6.3, 2.6.2, 2.6.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.
albert¶
- Homepage:
- Spack package:
- Versions:
- 4.0a_opt4
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- Albert is an interactive program to assist the specialist in the study of nonassociative algebra.
alglib¶
- Homepage:
- Spack package:
- Versions:
- 3.11.0
- Description:
- ALGLIB is a cross-platform numerical analysis and data processing library.
allinea-forge¶
- Homepage:
- Spack package:
- Versions:
- 6.0.4
- Description:
- Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
allinea-reports¶
- Homepage:
- Spack package:
- Versions:
- 6.0.4
- Description:
- Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site
allpaths-lg¶
- Homepage:
- Spack package:
- Versions:
- 52488
- Description:
- ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes.
alquimia¶
- Homepage:
- Spack package:
- Versions:
- develop, xsdk-0.3.0, xsdk-0.2.0
- Build Dependencies:
- cmake, hdf5, petsc, pflotran, mpi
- Link Dependencies:
- hdf5, petsc, pflotran, mpi
- Description:
- Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as CrunchFlow and PFLOTRAN
alsa-lib¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4.1
- Description:
- The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.
amg¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems.
amg2013¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- AMG2013 is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. It has been derived directly from the BoomerAMG solver in the hypre library, a large linear solver library that is being developed in the Center for Applied Scientific Computing (CASC) at LLNL.
amp¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- silo, trilinos, petsc, boost, mpi, lapack, zlib, cmake, hdf5, blas
- Link Dependencies:
- silo, trilinos, petsc, boost, mpi, lapack, zlib, hdf5, blas
- Description:
- The Advanced Multi-Physics (AMP) package is an open source parallel object-oriented computational framework that is designed with single and multi-domain multi-physics applications in mind. AMP can be used to build powerful and flexible multi-physics simulation algorithms from lightweight operator, solver, linear algebra, material database, discretization, and meshing components. The AMP design is meant to enable existing investments in application codes to be leveraged without having to adopt dramatically different data structures while developing new computational science applications. Application components are represented as discrete mathematical operators that only require a minimal interface and through operator composition the incremental development of complex parallel applications is enabled. AMP is meant to allow application domain scientists, computer scientists and mathematicians to simulate, collaborate, and conduct research on various aspects of massively parallel simulation algorithms.
ampliconnoise¶
- Homepage:
- Spack package:
- Versions:
- 1.29
- Build Dependencies:
- gsl, mpi
- Link Dependencies:
- gsl, mpi
- Description:
- AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.
amr-exp-parabolic¶
- Homepage:
- Spack package:
- Versions:
- release
- Build Dependencies:
- gmake, mpi
- Link Dependencies:
- mpi
- Description:
- Simplified block-structured adaptive mesh refinement algorithm in two and three dimensions with subcycling in time. The algorithm solves a linear advection diffusion equation with a simple numerical method. This proxy app is intended to capture the communication pattern of an explicit AMR algorithm but does not represent an accurate characterization of floating point effort or relative costs of communication to computation.
amrex¶
- Homepage:
- Spack package:
- Versions:
- develop, 17.06, master
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- AMReX is the successor to BoxLib. It is a Block-Structured AMR Framework.
andi¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- autoconf, m4, libtool, libdivsufsort, automake, gsl
- Link Dependencies:
- libdivsufsort, gsl
- Description:
- andi is used for for estimating the evolutionary distance between closely related genomes.
angsd¶
- Homepage:
- Spack package:
- Versions:
- 0.921, 0.919
- Build Dependencies:
- htslib
- Link Dependencies:
- htslib
- Description:
- Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
ant¶
- Homepage:
- Spack package:
- Versions:
- 1.9.9, 1.9.8, 1.9.7, 1.9.6
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other
antlr¶
- Homepage:
- Spack package:
- Versions:
- 2.7.7
- Build Dependencies:
- python, java
- Link Dependencies:
- python
- Run Dependencies:
- java
- Description:
- ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.
ape¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1
- Build Dependencies:
- libxc, gsl
- Link Dependencies:
- libxc, gsl
- Description:
- A tool for generating atomic pseudopotentials within a Density- Functional Theory framework
apex¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- cmake, binutils, ompt-openmp, boost, activeharmony
- Link Dependencies:
- binutils, ompt-openmp, boost, activeharmony
- Description:
applewmproto¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Apple Rootless Window Management Extension. This extension defines a protcol that allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.
appres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros, libxt
- Link Dependencies:
- libx11, libxt
- Description:
- The appres program prints the resources seen by an application (or subhierarchy of an application) with the specified class and instance names. It can be used to determine which resources a particular program will load.
apr-util¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0, 1.5.4
- Build Dependencies:
- unixodbc, openssl, apr, gdbm, libiconv, expat, postgresql, sqlite
- Link Dependencies:
- unixodbc, openssl, apr, gdbm, libiconv, expat, postgresql, sqlite
- Description:
- Apache Portable Runtime Utility
archer¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- ninja, cmake, llvm, llvm-openmp-ompt
- Link Dependencies:
- llvm, llvm-openmp-ompt
- Description:
- ARCHER, a data race detection tool for large OpenMP applications.
argp-standalone¶
- Homepage:
- Spack package:
- Versions:
- 1.3
- Description:
- Standalone version of the argp interface from glibc for parsing unix- style arguments.
argtable¶
- Homepage:
- Spack package:
- Versions:
- 2-13
- Description:
- Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
arlecore¶
- Homepage:
- Spack package:
- Versions:
- 3.5.2.2
- Build Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An Integrated Software for Population Genetics Data Analysis
armadillo¶
- Homepage:
- Spack package:
- Versions:
- 8.100.1, 7.950.1, 7.900.1, 7.500.0, 7.200.2, 7.200.1
- Build Dependencies:
- arpack-ng, hdf5, superlu, cmake, lapack, blas
- Link Dependencies:
- superlu, arpack-ng, hdf5, lapack, blas
- Description:
- Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.
arpack-ng¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0, 3.4.0, 3.3.0
- Build Dependencies:
- autoconf, libtool, mpi, lapack, automake, cmake, blas
- Link Dependencies:
- lapack, blas, mpi
- Description:
- ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.
ascent¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- py-numpy, conduit, py-mpi4py, py-sphinx, mpi, python, adios, cmake, vtkh
- Link Dependencies:
- adios, conduit, mpi, python, py-mpi4py, cmake, vtkh
- Run Dependencies:
- py-numpy
- Description:
- Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.
asciidoc¶
- Homepage:
- Spack package:
- Versions:
- 8.6.9
- Build Dependencies:
- libxslt, docbook-xml, docbook-xsl, libxml2
- Link Dependencies:
- libxslt, docbook-xml, docbook-xsl, libxml2
- Description:
- A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.
aspa¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- lapack, hdf5, blas, mpi
- Link Dependencies:
- lapack, hdf5, blas, mpi
- Description:
- A fundamental premise in ExMatEx is that scale-bridging performed in heterogeneous MPMD materials science simulations will place important demands upon the exascale ecosystem that need to be identified and quantified.
aspell¶
- Homepage:
- Spack package:
- Versions:
- 0.60.6.1
- Description:
- GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.
aspell6-de¶
- Homepage:
- Spack package:
- Versions:
- 6-de-20030222-1
- Build Dependencies:
- aspell
- Link Dependencies:
- aspell
- Description:
- German (de) dictionary for aspell.
aspell6-en¶
- Homepage:
- Spack package:
- Versions:
- 2017.01.22-0
- Build Dependencies:
- aspell
- Link Dependencies:
- aspell
- Description:
- English (en) dictionary for aspell.
aspell6-es¶
- Homepage:
- Spack package:
- Versions:
- 1.11-2
- Build Dependencies:
- aspell
- Link Dependencies:
- aspell
- Description:
- Spanish (es) dictionary for aspell.
assimp¶
- Homepage:
- Spack package:
- Versions:
- 4.0.1
- Build Dependencies:
- cmake, boost
- Link Dependencies:
- boost
- Description:
- Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner.
astra¶
- Homepage:
- Spack package:
- Versions:
- 2016-11-30
- Description:
- A Space Charge Tracking Algorithm.
astral¶
- Homepage:
- Spack package:
- Versions:
- 4.10.7
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.
astyle¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1, 2.06, 2.05.1, 2.04
- Description:
- A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.
atk¶
- Homepage:
- Spack package:
- Versions:
- 2.20.0, 2.14.0
- Build Dependencies:
- pkgconfig, gobject-introspection, glib
- Link Dependencies:
- gobject-introspection, glib
- Description:
- ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
atlas¶
- Homepage:
- Spack package:
- Versions:
- 3.11.39, 3.11.34, 3.10.3, 3.10.2
- Description:
- Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines in the LAPACK library.
atom-dft¶
- Homepage:
- Spack package:
- Versions:
- 4.2.6
- Build Dependencies:
- libgridxc, xmlf90
- Link Dependencies:
- libgridxc, xmlf90
- Description:
- ATOM is a program for DFT calculations in atoms and pseudopotential generation.
atompaw¶
- Homepage:
- Spack package:
- Versions:
- 4.0.0.13, 3.1.0.3
- Build Dependencies:
- lapack, libxc, blas
- Link Dependencies:
- lapack, libxc, blas
- Description:
- A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf
atop¶
- Homepage:
- Spack package:
- Versions:
- 2.2-3
- Build Dependencies:
- ncurses, zlib
- Link Dependencies:
- ncurses, zlib
- Description:
- Atop is an ASCII full-screen performance monitor for Linux
augustus¶
- Homepage:
- Spack package:
- Versions:
- 3.3, 3.2.3
- Build Dependencies:
- gsl, zlib, bamtools, boost
- Link Dependencies:
- gsl, zlib, bamtools, boost
- Description:
- AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
autoconf¶
- Homepage:
- Spack package:
- Versions:
- 2.69, 2.62, 2.59, 2.13
- Build Dependencies:
- perl, m4
- Run Dependencies:
- perl, m4
- Description:
- Autoconf -- system configuration part of autotools
autodock-vina¶
- Homepage:
- Spack package:
- Versions:
- 1_1_2
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Description:
- AutoDock Vina is an open-source program for doing molecular docking
autogen¶
- Homepage:
- Spack package:
- Versions:
- 5.18.12
- Build Dependencies:
- pkgconfig, guile, libxml2
- Link Dependencies:
- guile, libxml2
- Description:
- AutoGen is a tool designed to simplify the creation and maintenance of programs that contain large amounts of repetitious text. It is especially valuable in programs that have several blocks of text that must be kept synchronized.
automaded¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- callpath, cmake, boost, mpi
- Link Dependencies:
- callpath, boost, mpi
- Description:
- AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosis of performance and correctness problems in MPI applications. It creates control-flow models of each MPI process and, when a failure occurs, these models are leveraged to find the origin of problems automatically. MPI calls are intercepted (using wrappers) to create the models. When an MPI application hangs, AutomaDeD creates a progress-dependence graph that helps finding the process (or group of processes) that caused the hang.
automake¶
- Homepage:
- Spack package:
- Versions:
- 1.15.1, 1.15, 1.14.1, 1.11.6
- Build Dependencies:
- perl, autoconf
- Run Dependencies:
- perl
- Description:
- Automake -- make file builder part of autotools
bamtools¶
- Homepage:
- Spack package:
- Versions:
- 2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.3
- Build Dependencies:
- cmake
- Link Dependencies:
- zlib
- Description:
- C++ API & command-line toolkit for working with BAM data.
bamutil¶
- Homepage:
- Spack package:
- Versions:
- 1.0.13
- Description:
- bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
barrnap¶
- Homepage:
- Spack package:
- Versions:
- 0.8
- Run Dependencies:
- hmmer
- Description:
- Barrnap predicts the location of ribosomal RNA genes in genomes.
bash¶
- Homepage:
- Spack package:
- Versions:
- 4.4.12, 4.4, 4.3
- Build Dependencies:
- ncurses, readline
- Link Dependencies:
- ncurses, readline
- Description:
- The GNU Project's Bourne Again SHell.
bash-completion¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.7, 2.3
- Build Dependencies:
- automake, autoconf, libtool
- Run Dependencies:
- bash
- Description:
- Programmable completion functions for bash.
bats¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Description:
- Bats is a TAP-compliant testing framework for Bash.
bazel¶
- Homepage:
- Spack package:
- Versions:
- 0.4.5, 0.4.4, 0.3.1, 0.3.0, 0.2.3, 0.2.2b, 0.2.2
- Build Dependencies:
- zip, java
- Link Dependencies:
- zip, java
- Description:
- Bazel is Google's own build tool
bbcp¶
- Homepage:
- Spack package:
- Versions:
- git
- Build Dependencies:
- zlib, openssl
- Link Dependencies:
- zlib, openssl
- Description:
- Securely and quickly copy data from source to target
bbmap¶
- Homepage:
- Spack package:
- Versions:
- 37.36
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Short read aligner for DNA and RNA-seq data.
bcftools¶
- Homepage:
- Spack package:
- Versions:
- 1.6, 1.4, 1.3.1, 1.2
- Build Dependencies:
- htslib
- Link Dependencies:
- htslib
- Description:
- BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF- compressed.
bcl2fastq2¶
- Homepage:
- Spack package:
- Versions:
- 2.19.1.403, 2.18.0.12, 2.17.1.14
- Build Dependencies:
- libgcrypt, zlib, boost, libxslt, cmake, libxml2
- Link Dependencies:
- libgcrypt, zlib, boost, libxslt, cmake, libxml2
- Description:
- The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.
bdftopcf¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, xproto, libxfont, fontsproto, util-macros
- Link Dependencies:
- libxfont
- Description:
- bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines.
bdw-gc¶
- Homepage:
- Spack package:
- Versions:
- 7.6.0, 7.4.4
- Build Dependencies:
- libatomic-ops
- Link Dependencies:
- libatomic-ops
- Description:
- The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new.
bear¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.0.4
- Build Dependencies:
- cmake, python
- Link Dependencies:
- python
- Description:
- Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.
beast2¶
- Homepage:
- Spack package:
- Versions:
- 2.4.6
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time- measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
bedtools2¶
- Homepage:
- Spack package:
- Versions:
- 2.27.1, 2.27.0, 2.26.0, 2.25.0, 2.23.0
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
beforelight¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, libxscrnsaver, libx11, util-macros, libxt
- Link Dependencies:
- libxscrnsaver, libx11, libxt
- Description:
- The beforelight program is a sample implementation of a screen saver for X servers supporting the MIT-SCREEN-SAVER extension. It is only recommended for use as a code sample, as it does not include features such as screen locking or configurability.
benchmark¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.2.0, 1.1.0, 1.0.0
- Build Dependencies:
- cmake
- Description:
- A microbenchmark support library
berkeley-db¶
- Homepage:
- Spack package:
- Versions:
- 6.2.32, 6.1.29, 6.0.35, 5.3.28
- Description:
- Oracle Berkeley DB
bertini¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- flex, mpi, bison, mpfr, gmp
- Link Dependencies:
- mpi, mpfr, gmp
- Description:
- Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.
bib2xhtml¶
- Homepage:
- Spack package:
- Versions:
- 3.0-15-gf506
- Description:
- bib2xhtml is a program that converts BibTeX files into HTML.
bigreqsproto¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Big Requests Extension. This extension defines a protocol to enable the use of requests that exceed 262140 bytes in length.
binutils¶
- Homepage:
- Spack package:
- Versions:
- 2.29.1, 2.28, 2.27, 2.26, 2.25, 2.24, 2.23.2, 2.20.1
- Build Dependencies:
- zlib, m4, bison, gettext, flex
- Link Dependencies:
- zlib, gettext
- Description:
- GNU binutils, which contain the linker, assembler, objdump and others
bioawk¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- zlib, bison
- Link Dependencies:
- zlib
- Description:
- Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
biopieces¶
- Homepage:
- Spack package:
- Versions:
- 2016-04-12
- Build Dependencies:
- muscle, perl-xml-parser, perl-soap-lite, perl-inline, vmatch, perl-module-build, perl-svg, perl-term-readkey, blat, perl-carp-clan, perl-class-inspector, velvet, perl-inline-c, perl-dbd-mysql, perl-version, perl-dbi, ruby-rubyinline, perl-lwp, perl-time-hires, perl-dbfile, blast-plus, ruby, perl-uri, perl-html-parser, usearch, ruby-gnuplot, perl, idba, ruby-terminal-table, scan-for-matches, perl-parse-recdescent, bwa, bowtie, python, ruby-narray, perl-bit-vector, mummer, ray
- Link Dependencies:
- ruby-terminal-table, muscle, ruby-gnuplot, ruby, vmatch, usearch, blast-plus, idba, blat, scan-for-matches, velvet, bwa, bowtie, ruby-rubyinline, mummer, ruby-narray, ray
- Run Dependencies:
- perl-time-hires, perl-xml-parser, perl-soap-lite, perl-inline, perl-uri, perl, python, perl-module-build, perl-svg, perl-inline-c, perl-carp-clan, perl-class-inspector, perl-parse-recdescent, perl-html-parser, perl-term-readkey, perl-dbd-mysql, perl-version, perl-bit-vector, perl-dbi, perl-dbfile, perl-lwp
- Description:
- The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.
bison¶
- Homepage:
- Spack package:
- Versions:
- 3.0.4, 2.7
- Build Dependencies:
- m4
- Run Dependencies:
- m4
- Description:
- Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
bitmap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8
- Build Dependencies:
- xbitmaps, libx11, util-macros, libxt, pkgconfig, libxmu, libxaw, xproto
- Link Dependencies:
- libxmu, libxaw, libx11, libxt
- Description:
- bitmap, bmtoa, atobm - X bitmap (XBM) editor and converter utilities.
blast-plus¶
- Homepage:
- Spack package:
- Versions:
- 2.6.0, 2.2.30
- Build Dependencies:
- libpng, perl, openssl, zlib, bzip2, freetype, pcre, gnutls, python, lzo, jpeg
- Link Dependencies:
- libpng, perl, openssl, zlib, bzip2, freetype, pcre, gnutls, python, lzo, jpeg
- Description:
- Basic Local Alignment Search Tool.
blat¶
- Homepage:
- Spack package:
- Versions:
- 35
- Build Dependencies:
- libpng
- Link Dependencies:
- libpng
- Description:
- BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.
blaze¶
- Homepage:
- Spack package:
- Versions:
- 3.2, 3.1, 3.0, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0
- Description:
- Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain- specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.
bliss¶
- Homepage:
- Spack package:
- Versions:
- 0.73
- Build Dependencies:
- libtool, gmp
- Link Dependencies:
- gmp
- Description:
- bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs
bmake¶
- Homepage:
- Spack package:
- Versions:
- 20171207
- Description:
- bmake: portable BSD make bmake is the BSD make(1) utility ported to several non-BSD systems. It supports GNU's autoconf.
bml¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.2.2, 1.1.0
- Build Dependencies:
- lapack, blas, cmake, mpi
- Link Dependencies:
- lapack, blas, mpi
- Description:
- The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.
bohrium¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- py-numpy, zlib, opencl, python, cmake, cuda, opencv, boost, swig, blas, netlib-lapack, py-cython
- Link Dependencies:
- cuda, opencv, zlib, opencl, netlib-lapack, blas, python, boost
- Run Dependencies:
- py-numpy
- Test Dependencies:
- py-numpy, python
- Description:
- Library for automatic acceleration of array operations
boost¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.66.0, 1.65.1, 1.65.0, 1.64.0, 1.63.0, 1.62.0, 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0, 1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1, 1.34.0
- Build Dependencies:
- python, mpi, zlib, icu4c, bzip2
- Link Dependencies:
- python, mpi, zlib, icu4c, bzip2
- Description:
- Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
boostmplcartesianproduct¶
- Homepage:
- Spack package:
- Versions:
- 20161205
- Description:
- Cartesian_product is an extension to the Boost.MPL library and as such requires a version of the Boost libraries on your system.
bowtie¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- tbb
- Link Dependencies:
- tbb
- Description:
- Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
bowtie2¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1, 2.3.0, 2.2.5
- Build Dependencies:
- zlib, tbb, readline
- Link Dependencies:
- zlib, tbb, readline
- Run Dependencies:
- perl, python
- Description:
- Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
boxlib¶
- Homepage:
- Spack package:
- Versions:
- 16.12.2
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR) codes.
bpp-core¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- cmake
- Description:
- Bio++ core library.
bpp-phyl¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- bpp-seq, cmake, bpp-core
- Link Dependencies:
- bpp-seq, bpp-core
- Description:
- Bio++ phylogeny library.
bpp-seq¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- cmake, bpp-core
- Link Dependencies:
- bpp-core
- Description:
- Bio++ seq library.
bpp-suite¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- bpp-phyl, bpp-seq, cmake, texinfo, bpp-core
- Link Dependencies:
- bpp-phyl, bpp-seq, bpp-core
- Description:
- BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
braker¶
- Homepage:
- Spack package:
- Versions:
- 1.11
- Build Dependencies:
- perl, augustus, samtools, genemark-et, bamtools
- Link Dependencies:
- augustus, samtools, genemark-et, bamtools
- Run Dependencies:
- perl
- Description:
- BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS
branson¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.01
- Build Dependencies:
- metis, mpi, cmake, boost, parmetis
- Link Dependencies:
- metis, mpi, boost, parmetis
- Description:
- Branson's purpose is to study different algorithms for parallel Monte Carlo transport. Currently it contains particle passing and mesh passing methods for domain decomposition.
breakdancer¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake, zlib
- Link Dependencies:
- zlib
- Description:
- BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs..
breseq¶
- Homepage:
- Spack package:
- Versions:
- 0.31.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Run Dependencies:
- r, bedtools2
- Description:
- breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.
brigand¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0, 1.2.0, 1.1.0, 1.0.0, master
- Description:
- Brigand Meta-programming library
bsseeker2¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2
- Build Dependencies:
- py-pysam, python
- Run Dependencies:
- py-pysam, python
- Description:
- A versatile aligning pipeline for bisulfite sequencing data.
bucky¶
- Homepage:
- Spack package:
- Versions:
- 1.4.4
- Description:
- BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.
busco¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1, 2.0.1
- Build Dependencies:
- hmmer, augustus, python, blast-plus
- Link Dependencies:
- hmmer, augustus, python, blast-plus
- Run Dependencies:
- python
- Description:
- Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
butter¶
- Homepage:
- Spack package:
- Versions:
- 0.3.3
- Build Dependencies:
- perl, samtools, bowtie
- Link Dependencies:
- samtools, bowtie
- Run Dependencies:
- perl
- Description:
- butter: Bowtie UTilizing iTerative placEment of Repetitive small rnas. A wrapper for bowtie to produce small RNA-seq alignments where multimapped small RNAs tend to be placed near regions of confidently high density.
bwa¶
- Homepage:
- Spack package:
- Versions:
- 0.7.17, 0.7.16a, 0.7.15, 0.7.13, 0.7.12
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
byobu¶
- Homepage:
- Spack package:
- Versions:
- 5.123
- Build Dependencies:
- tmux
- Run Dependencies:
- tmux
- Description:
- Byobu: Text-based window manager and terminal multiplexer.
bzip2¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Description:
- bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
c-blosc¶
- Homepage:
- Spack package:
- Versions:
- 1.12.1, 1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
- Build Dependencies:
- cmake, lz4, zlib, snappy, zstd
- Link Dependencies:
- lz4, zlib, snappy, zstd
- Description:
- Blosc, an extremely fast, multi-threaded, meta-compressor library
caffe¶
- Homepage:
- Spack package:
- Versions:
- 1.0, rc5, rc4, rc3, rc2
- Build Dependencies:
- py-numpy, matlab, hdf5, glog, protobuf, cmake, lmdb, gflags, cuda, opencv, boost, python, leveldb, blas
- Link Dependencies:
- matlab, hdf5, glog, protobuf, lmdb, gflags, cuda, opencv, boost, python, leveldb, blas
- Run Dependencies:
- py-numpy
- Description:
- Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors.
cairo¶
- Homepage:
- Spack package:
- Versions:
- 1.14.12, 1.14.8, 1.14.0
- Build Dependencies:
- libpng, libxext, libxrender, freetype, libx11, fontconfig, pkgconfig, python, pixman, glib, libxcb
- Link Dependencies:
- libpng, libxext, libxrender, freetype, libx11, fontconfig, glib, pixman, libxcb
- Description:
- Cairo is a 2D graphics library with support for multiple output devices.
caliper¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0, master
- Build Dependencies:
- libpfm4, libunwind, sosflow, mpi, cmake, dyninst, papi, python
- Link Dependencies:
- libpfm4, libunwind, sosflow, mpi, dyninst, papi
- Description:
- Caliper is a program instrumentation and performance measurement framework. It provides data collection mechanisms and a source-code annotation API for a variety of performance engineering use cases, e.g., performance profiling, tracing, monitoring, and auto-tuning.
callpath¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4, 1.0.2, 1.0.1
- Build Dependencies:
- adept-utils, dyninst, cmake, libdwarf, mpi
- Link Dependencies:
- adept-utils, dyninst, libdwarf, elf, mpi
- Description:
- Library for representing callpaths consistently in distributed-memory performance tools.
candle-benchmarks¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- py-scikit-learn, python, py-mpi4py, opencv, py-keras, py-matplotlib, py-theano, py-h5py, py-mdanalysis, py-tqdm
- Link Dependencies:
- opencv, python
- Run Dependencies:
- py-scikit-learn, py-mpi4py, py-keras, py-matplotlib, py-theano, py-h5py, py-mdanalysis, py-tqdm
- Description:
- ECP-CANDLE Benchmarks
cantera¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0, 2.2.1
- Build Dependencies:
- py-numpy, sundials, py-scipy, matlab, lapack, python, fmt, boost, scons, py-cython, eigen, py-3to2, googletest, blas
- Link Dependencies:
- fmt, sundials, boost, matlab, lapack, eigen, python, googletest, blas
- Run Dependencies:
- py-numpy, py-3to2, py-scipy
- Description:
- Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.
canu¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Run Dependencies:
- gnuplot, perl, jdk
- Description:
- A single molecule sequence assembler for genomes large and small.
cap3¶
- Homepage:
- Spack package:
- Versions:
- 2015-02-11
- Description:
- CAP3 is DNA Sequence Assembly Program
cares¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.13.0
- Build Dependencies:
- cmake
- Description:
- c-ares: A C library for asynchronous DNS requests
cask¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1, 0.7.4
- Build Dependencies:
- emacs
- Run Dependencies:
- emacs
- Description:
- Cask is a project management tool for Emacs Lisp to automate the package development cycle; development, dependencies, testing, building, packaging and more.
casper¶
- Homepage:
- Spack package:
- Versions:
- 0.8.2
- Build Dependencies:
- jellyfish, boost
- Link Dependencies:
- jellyfish, boost
- Description:
- CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.
catalyst¶
- Homepage:
- Spack package:
- Versions:
- 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
- Build Dependencies:
- libx11, libxt, cmake, mpi, python, mesa, git
- Link Dependencies:
- libx11, libxt, mpi, python, mesa, git
- Description:
- Catalyst is an in situ use case library, with an adaptable application programming interface (API), that orchestrates the alliance between simulation and analysis and/or visualization tasks.
catch¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 2.0.1, 1.12.0, 1.11.0, 1.10.0, 1.9.7, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.8.1, 1.8.0, 1.7.2, 1.7.1, 1.7.0, 1.6.1, 1.6.0, 1.5.9, 1.5.0, 1.4.0, 1.3.5, 1.3.0
- Description:
- Catch tests
cbench¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- lapack, fftw, mpi, blas
- Link Dependencies:
- lapack, fftw, mpi, blas
- Description:
- Cbench is intended as a relatively straightforward toolbox of tests, benchmarks, applications, utilities, and framework to hold them together with the goal to facilitate scalable testing, benchmarking, and analysis of a Linux parallel compute cluster.
cblas¶
- Homepage:
- Spack package:
- Versions:
- 2015-06-06
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.
cbtf¶
- Homepage:
- Spack package:
- Versions:
- 1.8
- Build Dependencies:
- mrnet, cmake, boost, xerces-c, libxml2
- Link Dependencies:
- mrnet, boost, xerces-c, libxml2
- Description:
- CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.
cbtf-krell¶
- Homepage:
- Spack package:
- Versions:
- 1.8
- Build Dependencies:
- libmonitor, libunwind, papi, mpt, openmpi, dyninst, binutils, llvm-openmp-ompt, mvapich2, xerces-c, mrnet, mvapich, boost, mpich, cmake, mpich2, cbtf
- Link Dependencies:
- libmonitor, libunwind, papi, mpt, openmpi, dyninst, binutils, llvm-openmp-ompt, mvapich2, xerces-c, mrnet, mvapich, boost, mpich, mpich2, cbtf
- Description:
- CBTF Krell project contains the Krell Institute contributions to the CBTF project. These contributions include many performance data collectors and support libraries as well as some example tools that drive the data collection at HPC levels of scale.
cbtf-lanl¶
- Homepage:
- Spack package:
- Versions:
- 1.8
- Build Dependencies:
- xerces-c, cmake, cbtf-krell, cbtf, mrnet
- Link Dependencies:
- xerces-c, cbtf-krell, cbtf, mrnet
- Description:
- CBTF LANL project contains a memory tool and data center type system command monitoring tool.
ccache¶
- Homepage:
- Spack package:
- Versions:
- 3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3, 3.2.9
- Build Dependencies:
- libxslt, gperf, zlib
- Link Dependencies:
- libxslt, gperf, zlib
- Description:
- ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again.
cctools¶
- Homepage:
- Spack package:
- Versions:
- 6.1.1
- Build Dependencies:
- perl, openssl, swig, zlib, python, readline
- Link Dependencies:
- swig, openssl, zlib, readline
- Run Dependencies:
- perl, python
- Description:
- The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.
cdbfasta¶
- Homepage:
- Spack package:
- Versions:
- 2017-03-16
- Description:
- Fast indexing and retrieval of fasta records from flat file databases
cdd¶
- Homepage:
- Spack package:
- Versions:
- 0.61a
- Build Dependencies:
- libtool
- Description:
- The program cdd+ (cdd, respectively) is a C++ (ANSI C) implementation of the Double Description Method [MRTT53] for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron given by a system of linear inequalities
cddlib¶
- Homepage:
- Spack package:
- Versions:
- 0.94h
- Build Dependencies:
- libtool, gmp
- Link Dependencies:
- gmp
- Description:
- The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by a system of linear inequalities
cdhit¶
- Homepage:
- Spack package:
- Versions:
- 4.6.8
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cdo¶
- Homepage:
- Spack package:
- Versions:
- 1.9.1, 1.9.0, 1.8.2, 1.7.2
- Build Dependencies:
- netcdf, hdf5, magics, udunits2, curl, grib-api, eccodes, szip, libxml2, fftw, proj, libuuid
- Link Dependencies:
- netcdf, hdf5, magics, udunits2, curl, grib-api, eccodes, szip, libxml2, fftw, proj, libuuid
- Description:
- CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
cereal¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0, 1.0.0, 0.9.1
- Build Dependencies:
- cmake
- Description:
- cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
cfitsio¶
- Homepage:
- Spack package:
- Versions:
- 3.420, 3.410, 3.370
- Build Dependencies:
- bzip2
- Link Dependencies:
- bzip2
- Description:
- CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
cgal¶
- Homepage:
- Spack package:
- Versions:
- 4.11, 4.9.1, 4.9, 4.7, 4.6.3
- Build Dependencies:
- zlib, boost, mpfr, qt, cmake, gmp
- Link Dependencies:
- qt, gmp, zlib, boost, mpfr
- Description:
- The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
cgm¶
- Homepage:
- Spack package:
- Versions:
- 16.0, 13.1.1, 13.1.0, 13.1
- Build Dependencies:
- oce, mpi
- Link Dependencies:
- oce, mpi
- Description:
- The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry functionality used for mesh generation and other applications.
cgns¶
- Homepage:
- Spack package:
- Versions:
- 3.3.1, 3.3.0
- Build Dependencies:
- hdf5, cmake, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.
charm¶
- Homepage:
- Spack package:
- Versions:
- 6.7.1, 6.7.0, 6.6.1, 6.6.0, 6.5.1
- Build Dependencies:
- papi, mpi
- Link Dependencies:
- papi, mpi
- Description:
- Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.
check¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0
- Description:
- Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.
chlorop¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Run Dependencies:
- awk
- Description:
- Chlorop predicts the presence of chloroplast transit peptides in protein sequences and the location of potential cTP cleavage sites. You will need to obtain the tarball by visiting the URL and completing the form. You can then either run spack install with the tarball in the directory, or add it to a mirror. You will need to set the CHLOROTMP environment variable to the full path of the directory you want chlorop to use as a temporary directory.
chombo¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.2
- Build Dependencies:
- lapack, blas, hdf5, gmake, mpi
- Link Dependencies:
- lapack, hdf5, blas, mpi
- Description:
- The Chombo package provides a set of tools for implementing finite difference and finite-volume methods for the solution of partial differential equations on block-structured adaptively refined logically rectangular (i.e. Cartesian) grids.
cityhash¶
- Homepage:
- Spack package:
- Versions:
- 2013-07-31, master
- Description:
- CityHash, a family of hash functions for strings.
clamr¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake, mpe, mpi
- Link Dependencies:
- mpe, mpi
- Description:
- The CLAMR code is a cell-based adaptive mesh refinement (AMR) mini-app developed as a testbed for hybrid algorithm development using MPI and OpenCL GPU code.
cleaveland4¶
- Homepage:
- Spack package:
- Versions:
- 4.4
- Build Dependencies:
- perl, perl-math-cdf, viennarna, samtools, r, bowtie
- Link Dependencies:
- viennarna, samtools, bowtie
- Run Dependencies:
- perl, perl-math-cdf, r
- Description:
- CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets
cleverleaf¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- samrai, hdf5, cmake, boost
- Link Dependencies:
- samrai, hdf5, boost
- Description:
- CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National Laboratory. The primary goal of CleverLeaf is to evaluate the application of AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.
clfft¶
- Homepage:
- Spack package:
- Versions:
- 2.12.2
- Build Dependencies:
- cmake, opencl, boost
- Link Dependencies:
- opencl, boost
- Description:
- a software library containing FFT functions written in OpenCL
clhep¶
- Homepage:
- Spack package:
- Versions:
- 2.4.0.1, 2.4.0.0, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.4.1, 2.3.4.0, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 2.3.2.1, 2.3.1.1, 2.3.1.0, 2.3.0.0, 2.2.0.8, 2.2.0.5, 2.2.0.4
- Build Dependencies:
- cmake
- Description:
- CLHEP is a C++ Class Library for High Energy Physics.
clingo¶
- Homepage:
- Spack package:
- Versions:
- 5.2.2
- Build Dependencies:
- cmake, doxygen, python
- Link Dependencies:
- python
- Description:
- Clingo: A grounder and solver for logic programs Clingo is part of the Potassco project for Answer Set Programming (ASP). ASP offers a simple and powerful modeling language to describe combinatorial problems as logic programs. The clingo system then takes such a logic program and computes answer sets representing solutions to the given problem.
cloc¶
- Homepage:
- Spack package:
- Versions:
- 1.74
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Description:
- Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.
cloog¶
- Homepage:
- Spack package:
- Versions:
- 0.18.1, 0.18.0, 0.17.0
- Build Dependencies:
- isl, gmp
- Link Dependencies:
- isl, gmp
- Description:
- CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra.
cloverleaf¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- cuda, mpi
- Link Dependencies:
- cuda, mpi
- Description:
- Proxy Application. CloverLeaf is a miniapp that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.
cloverleaf3d¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. CloverLeaf3D is 3D version of the CloverLeaf mini- app. CloverLeaf is a mini-app that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.
clustalo¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4
- Build Dependencies:
- argtable
- Link Dependencies:
- argtable
- Description:
- Clustal Omega: the last alignment program you'll ever need.
clustalw¶
- Homepage:
- Spack package:
- Versions:
- 2.1
- Description:
- Multiple alignment of nucleic acid and protein sequences.
cmake¶
- Homepage:
- Spack package:
- Versions:
- 3.10.1, 3.10.0, 3.9.4, 3.9.0, 3.8.2, 3.8.1, 3.8.0, 3.7.2, 3.7.1, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.4.0, 3.3.1, 3.1.0, 3.0.2, 2.8.10.2
- Build Dependencies:
- zlib, libuv, libarchive, qt, curl, rhash, xz, ncurses, openssl, py-sphinx, bzip2, expat, python
- Link Dependencies:
- ncurses, zlib, libuv, bzip2, libarchive, openssl, qt, curl, rhash, expat, xz
- Description:
- A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
cmocka¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1, 1.1.0, 1.0.1
- Build Dependencies:
- cmake
- Description:
- Unit-testing framework in pure C
cmor¶
- Homepage:
- Spack package:
- Versions:
- 3.2.0, 3.1.2
- Build Dependencies:
- netcdf, py-numpy, hdf5, uuid, udunits2, python
- Link Dependencies:
- netcdf, python, hdf5, uuid, udunits2
- Run Dependencies:
- py-numpy
- Description:
- Climate Model Output Rewriter is used to produce CF-compliant netCDF files. The structure of the files created by the library and the metadata they contain fulfill the requirements of many of the climate community's standard model experiments.
cnmem¶
- Homepage:
- Spack package:
- Versions:
- git
- Build Dependencies:
- cmake
- Description:
- CNMem mempool for CUDA devices
cnpy¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cmake
- Description:
- cnpy: library to read/write .npy and .npz files in C/C++.
cns-nospec¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- gmake, mpi
- Link Dependencies:
- mpi
- Description:
- A simple, explicit, stencil-based test code for integrating the compressible Navier-Stokes equations. The code uses 8th order finite differences in space and a 3rd order, low-storage TVD RK algorithm in time.
cntk¶
- Homepage:
- Spack package:
- Versions:
- 2.0, master
- Build Dependencies:
- libzip, protobuf, cub, cudnn, cuda, opencv, multiverso, openblas, kaldi, mpi, nccl, cntk1bitsgd, boost
- Link Dependencies:
- libzip, protobuf, cub, cudnn, cuda, opencv, multiverso, openblas, kaldi, mpi, nccl, cntk1bitsgd, boost
- Description:
- The Microsoft Cognitive Toolkit is a unified deep-learning toolkit that describes neural networks as a series of computational steps via a directed graph.
cntk1bitsgd¶
- Homepage:
- Spack package:
- Versions:
- master, c8b77d
- Description:
- CNTK1bitSGD is the header-only 1-bit stochastic gradient descent (1bit- SGD) library for the Computational Network Toolkit (CNTK).
codar-cheetah¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.1
- Build Dependencies:
- savanna, python
- Link Dependencies:
- savanna
- Run Dependencies:
- python
- Description:
- CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications.
coevp¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- lapack, silo, flann, mpi
- Link Dependencies:
- lapack, silo, flann, mpi
- Description:
- CoEVP is a scale-bridging proxy application for embedded viscoplasticity applications. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. Due to the size and complexity of the studied models, as well as restrictions on distribution, the currently available LULESH proxy application provides the coarse-scale model implementation and the ASPA proxy application provides the adaptive sampling support.
cohmm¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- gnuplot
- Link Dependencies:
- gnuplot
- Description:
- An anticipated important use-case for next-generation supercomputing is multiscale modeling, in which continuum equations for large-scale material deformation are augmented with high-fidelity, fine-scale simulations that provide constitutive data on demand.
coinhsl¶
- Homepage:
- Spack package:
- Versions:
- 2014.01.17, 2014.01.10
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- CoinHSL is a collection of linear algebra libraries (KB22, MA27, MA28, MA54, MA57, MA64, MA77, MA86, MA97, MC19, MC34, MC64, MC68, MC69, MC78, MC80, OF01, ZB01, ZB11) bundled for use with IPOPT and other applications that use these HSL routines. Note: CoinHSL is licensed software. You will need to request a license from Research Councils UK and download a .tar.gz archive of CoinHSL yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
comd¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1
- Build Dependencies:
- mpi, graphviz
- Link Dependencies:
- mpi, graphviz
- Description:
- CoMD is a reference implementation of classical molecular dynamics algorithms and workloads as used in materials science. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. New versions of CoMD will be released to incorporate the lessons learned from the co-design process.
compiz¶
- Homepage:
- Spack package:
- Versions:
- 0.7.8
- Build Dependencies:
- libpng, libxcomposite, libxdamage, libxfixes, glib, libxml2, libxslt, libxrandr, libsm, libxrender, libxinerama, gconf, libxcb, libice
- Link Dependencies:
- libpng, libxcomposite, libxdamage, libxfixes, glib, libxml2, libxslt, libxrandr, libsm, libxrender, libxinerama, gconf, libxcb, libice
- Description:
- compiz - OpenGL window and compositing manager. Compiz is an OpenGL compositing manager that use GLX_EXT_texture_from_pixmap for binding redirected top-level windows to texture objects. It has a flexible plug- in system and it is designed to run well on most graphics hardware.
compositeproto¶
- Homepage:
- Spack package:
- Versions:
- 0.4.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Composite Extension. This package contains header files and documentation for the composite extension. Library and server implementations are separate.
conduit¶
- Homepage:
- Spack package:
- Versions:
- 0.3.0, 0.2.1, 0.2.0, master
- Build Dependencies:
- py-numpy, silo, hdf5, doxygen, py-sphinx, mpi, python, cmake
- Link Dependencies:
- silo, hdf5, doxygen, mpi, python, cmake
- Run Dependencies:
- py-numpy
- Description:
- Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.
constype¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- constype prints on the standard output the Sun code for the type of display that the specified device is. It was originally written for SunOS, but has been ported to other SPARC OS'es and to Solaris on both SPARC & x86.
converge¶
- Homepage:
- Spack package:
- Versions:
- 2.4.10, 2.3.23, 2.2.0, 2.1.0, 2.0.0
- Build Dependencies:
- openmpi, mpi
- Link Dependencies:
- openmpi, mpi
- Description:
- CONVERGE is a revolutionary computational fluid dynamics (CFD) program that eliminates the grid generation bottleneck from the simulation process. CONVERGE was developed by engine simulation experts and is straightforward to use for both engine and non-engine simulations. Unlike many CFD programs, CONVERGE automatically generates a perfectly orthogonal, structured grid at runtime based on simple, user-defined grid control parameters. This grid generation method completely eliminates the need to manually generate a grid. In addition, CONVERGE offers many other features to expedite the setup process and to ensure that your simulations are as computationally efficient as possible.
coreutils¶
- Homepage:
- Spack package:
- Versions:
- 8.26, 8.23
- Description:
- The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
corset¶
- Homepage:
- Spack package:
- Versions:
- 1.06
- Description:
- Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.
cosmomc¶
- Homepage:
- Spack package:
- Versions:
- 2016.11, 2016.06
- Build Dependencies:
- py-numpy, py-pandas, py-scipy, planck-likelihood, mpi, py-matplotlib, python, py-six
- Link Dependencies:
- python, planck-likelihood, mpi
- Run Dependencies:
- py-numpy, py-pandas, py-scipy, py-matplotlib, python, py-six
- Description:
- CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine for exploring cosmological parameter space, together with Fortran and python code for analysing Monte-Carlo samples and importance sampling (plus a suite of scripts for building grids of runs, plotting and presenting results).
cosp2¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. CoSP2 represents a sparse linear algebra parallel algorithm for calculating the density matrix in electronic tructure theory. The algorithm is based on a recursive second-order Fermi- Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of non-metallic systems.
cp2k¶
- Homepage:
- Spack package:
- Versions:
- 5.1, 4.1, 3.0
- Build Dependencies:
- wannier90, fftw, lapack, scalapack, libint, elpa, libxsmm, libxc, pexsi, mpi, python, plumed, blas
- Link Dependencies:
- wannier90, fftw, lapack, scalapack, libint, elpa, libxsmm, libxc, pexsi, mpi, plumed, blas
- Description:
- CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems
cppad¶
- Homepage:
- Spack package:
- Versions:
- develop, 20170114
- Build Dependencies:
- cmake
- Description:
- A Package for Differentiation of C++ Algorithms.
cppcheck¶
- Homepage:
- Spack package:
- Versions:
- 1.81, 1.78, 1.72, 1.68
- Description:
- A tool for static C/C++ code analysis.
cpprestsdk¶
- Homepage:
- Spack package:
- Versions:
- 2.9.1
- Build Dependencies:
- cmake, boost
- Link Dependencies:
- boost
- Description:
- The C++ REST SDK is a Microsoft project for cloud-based client-server communication in native code using a modern asynchronous C++ API design. This project aims to help C++ developers connect to and interact with services.
cppunit¶
- Homepage:
- Spack package:
- Versions:
- 1.13.2
- Description:
- Obsolete Unit testing framework for C++
cppzmq¶
- Homepage:
- Spack package:
- Versions:
- develop, 4.2.2
- Build Dependencies:
- zeromq, cmake
- Link Dependencies:
- zeromq
- Description:
- C++ binding for 0MQ
cram¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- cmake, python, mpi
- Link Dependencies:
- python, mpi
- Description:
- Cram runs many small MPI jobs inside one large MPI job.
cryptopp¶
- Homepage:
- Spack package:
- Versions:
- 5.6.3, 5.6.2, 5.6.1
- Description:
- Crypto++ is an open-source C++ library of cryptographic schemes. The library supports a number of different cryptography algorithms, including authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama).
cscope¶
- Homepage:
- Spack package:
- Versions:
- 15.8b
- Build Dependencies:
- pkgconfig, ncurses, bison, flex
- Link Dependencies:
- ncurses
- Description:
- Cscope is a developer's tool for browsing source code.
csdp¶
- Homepage:
- Spack package:
- Versions:
- 6.1.1
- Build Dependencies:
- atlas
- Link Dependencies:
- atlas
- Description:
- CSDP is a library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz
ctffind¶
- Homepage:
- Spack package:
- Versions:
- 4.1.8
- Build Dependencies:
- fftw, wx
- Link Dependencies:
- fftw, wx
- Description:
- Fast and accurate defocus estimation from electron micrographs.
cub¶
- Homepage:
- Spack package:
- Versions:
- 1.7.1, 1.6.4, 1.4.1
- Description:
- CUB is a C++ header library of cooperative threadblock primitives and other utilities for CUDA kernel programming.
cube¶
- Homepage:
- Spack package:
- Versions:
- 4.3.5, 4.3.4, 4.3.3, 4.2.3
- Build Dependencies:
- qt, zlib
- Link Dependencies:
- qt, zlib
- Description:
- Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource
cuda¶
- Homepage:
- Spack package:
- Versions:
- 9.1.85, 9.0.176, 8.0.61, 8.0.44, 7.5.18, 6.5.14
- Description:
- CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. See: http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.
cuda-memtest¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cuda, cmake
- Link Dependencies:
- cuda
- Description:
- Maintained and updated fork of cuda_memtest. original homepage: http://sourceforge.net/projects/cudagpumemtest . This software tests GPU memory for hardware errors and soft errors using CUDA or OpenCL.
cudnn¶
- Homepage:
- Spack package:
- Versions:
- 6.0, 5.1
- Build Dependencies:
- cuda
- Link Dependencies:
- cuda
- Description:
- NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks
cufflinks¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1
- Description:
- Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
cups¶
- Homepage:
- Spack package:
- Versions:
- 2.2.3
- Build Dependencies:
- gnutls
- Link Dependencies:
- gnutls
- Description:
- CUPS is the standards-based, open source printing system developed by Apple Inc. for macOS and other UNIX-like operating systems. CUPS uses the Internet Printing Protocol (IPP) to support printing to local and network printers. This provides the core CUPS libraries, not a complete CUPS install.
curl¶
- Homepage:
- Spack package:
- Versions:
- 7.56.0, 7.54.0, 7.53.1, 7.52.1, 7.50.3, 7.50.2, 7.50.1, 7.49.1, 7.47.1, 7.46.0, 7.45.0, 7.44.0, 7.43.0, 7.42.1
- Build Dependencies:
- openssl, nghttp2, zlib
- Link Dependencies:
- openssl, nghttp2, zlib
- Description:
- cURL is an open source command line tool and library for transferring data with URL syntax
cvs¶
- Homepage:
- Spack package:
- Versions:
- 1.12.13
- Description:
- CVS a very traditional source control system
czmq¶
- Homepage:
- Spack package:
- Versions:
- 4.0.2, 3.0.2
- Build Dependencies:
- pkgconfig, automake, autoconf, zeromq, libtool
- Link Dependencies:
- zeromq
- Description:
- A C interface to the ZMQ library
dakota¶
- Homepage:
- Spack package:
- Versions:
- 6.3
- Build Dependencies:
- boost, mpi, lapack, cmake, python, blas
- Link Dependencies:
- lapack, blas, python, boost, mpi
- Description:
- The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods. Dakota contains algorithms for: - optimization with gradient and non gradient-based methods; - uncertainty quantification with sampling, reliability, stochastic - expansion, and epistemic methods; - parameter estimation with nonlinear least squares methods; - sensitivity/variance analysis with design of experiments and - parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.
daligner¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Description:
- Daligner: The Dazzler "Overlap" Module.
damageproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Damage Extension. This package contains header files and documentation for the X Damage extension. Library and server implementations are separate.
damselfly¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- cmake
- Description:
- Damselfly is a model-based parallel network simulator.
darshan-runtime¶
- Homepage:
- Spack package:
- Versions:
- 3.1.0, 3.0.0
- Build Dependencies:
- zlib, mpi
- Link Dependencies:
- zlib, mpi
- Description:
- Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. DarshanRuntime package should be installed on systems where you intend to instrument MPI applications.
darshan-util¶
- Homepage:
- Spack package:
- Versions:
- 3.1.0, 3.0.0
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Darshan (util) is collection of tools for parsing and summarizing log files produced by Darshan (runtime) instrumentation. This package is typically installed on systems (front-end) where you intend to analyze log files produced by Darshan (runtime).
dash¶
- Homepage:
- Spack package:
- Versions:
- 0.5.9.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Link Dependencies:
- libedit
- Description:
- The Debian Almquist Shell.
datamash¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0, 1.0.7, 1.0.6, 1.0.5
- Description:
- GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.
dataspaces¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.6.2
- Build Dependencies:
- automake, autoconf, m4, libtool, mpi
- Link Dependencies:
- mpi
- Description:
- an extreme scale data management framework.
dbus¶
- Homepage:
- Spack package:
- Versions:
- 1.11.2, 1.9.0, 1.8.8, 1.8.6, 1.8.4, 1.8.2
- Build Dependencies:
- expat
- Link Dependencies:
- expat
- Description:
- D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon).
dealii¶
- Homepage:
- Spack package:
- Versions:
- develop, 8.5.1, 8.5.0, 8.4.2, 8.4.1, 8.4.0, 8.3.0, 8.2.1, 8.1.0
- Build Dependencies:
- assimp, hdf5, zlib, gmsh, lapack, muparser, graphviz, suite-sparse, metis, cuda, slepc, trilinos, boost, netcdf-cxx, adol-c, netcdf, sundials, nanoflann, tbb, oce, gsl, scalapack, cmake, p4est, arpack-ng, doxygen, petsc, bzip2, python, mpi, blas
- Link Dependencies:
- assimp, hdf5, zlib, lapack, muparser, graphviz, suite-sparse, metis, cuda, slepc, trilinos, boost, netcdf-cxx, adol-c, netcdf, sundials, nanoflann, tbb, oce, gsl, scalapack, cmake, p4est, arpack-ng, doxygen, petsc, bzip2, python, mpi, blas
- Run Dependencies:
- gmsh
- Description:
- C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.
dejagnu¶
- Homepage:
- Spack package:
- Versions:
- 1.6, 1.4.4
- Build Dependencies:
- tcl, expect
- Link Dependencies:
- tcl, expect
- Description:
- DejaGnu is a framework for testing other programs. Its purpose is to provide a single front end for all tests.
delly2¶
- Homepage:
- Spack package:
- Versions:
- 2017-08-03
- Build Dependencies:
- bcftools, htslib, boost
- Link Dependencies:
- bcftools, htslib, boost
- Description:
- Delly2 is an integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short- read massively parallel sequencing data..
denovogear¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1, 1.1.0
- Build Dependencies:
- cmake, eigen, htslib, boost
- Description:
- DeNovoGear is a software package to detect de novo mutations using next- generation sequencing data. It supports the analysis of many differential experimental designs and uses advanced statistical models to reduce the false positve rate.
dia¶
- Homepage:
- Spack package:
- Versions:
- 0.97.3
- Build Dependencies:
- gtkplus, libxrender, freetype, libsm, libxslt, swig, libuuid, intltool, python, libxinerama, libxml2
- Link Dependencies:
- gtkplus, libxrender, freetype, libsm, libxslt, swig, libuuid, python, libxinerama, libxml2
- Description:
- Dia is a program for drawing structured diagrams.
dialign-tx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Description:
- DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
diamond¶
- Homepage:
- Spack package:
- Versions:
- 0.9.14
- Build Dependencies:
- cmake
- Description:
- DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
direnv¶
- Homepage:
- Spack package:
- Versions:
- 2.11.3
- Build Dependencies:
- go
- Description:
- direnv is an environment switcher for the shell.
discovar¶
- Homepage:
- Spack package:
- Versions:
- 52488
- Description:
- DISCOVAR is a variant caller and small genome assembler.
discovardenovo¶
- Homepage:
- Spack package:
- Versions:
- 52488
- Build Dependencies:
- samtools, jemalloc
- Link Dependencies:
- samtools, jemalloc
- Description:
- DISCOVAR de novo is a large (and small) de novo genome assembler. It quickly generates highly accurate and complete assemblies using the same single library data as used by DISCOVAR. It currently doesn't support variant calling, for that, please use DISCOVAR instead.
dlpack¶
- Homepage:
- Spack package:
- Versions:
- master
- Description:
- DLPack is an RFC for common tensor and operator guidelines in deep learning systems.
dmlc-core¶
- Homepage:
- Spack package:
- Versions:
- 20170508, master
- Build Dependencies:
- cmake
- Description:
- DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.
dmxproto¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Distributed Multihead X (DMX) Extension. This extension defines a protocol for clients to access a front-end proxy X server that controls multiple back-end X servers making up a large display.
docbook-xsl¶
- Homepage:
- Spack package:
- Versions:
- 1.79.1
- Build Dependencies:
- docbook-xml
- Link Dependencies:
- docbook-xml
- Description:
- Docbook XSL vocabulary.
dos2unix¶
- Homepage:
- Spack package:
- Versions:
- 7.3.4
- Description:
- DOS/Mac to Unix and vice versa text file format converter.
double-conversion¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1, 2.0.0, 1.1.5, 1.1.4, 1.1.3
- Build Dependencies:
- cmake
- Description:
- This project (double-conversion) provides binary-decimal and decimal- binary routines for IEEE doubles. The library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine. The code has been refactored and improved so that it can be used more easily in other projects. There is extensive documentation in src/double-conversion.h. Other examples can be found in test/cctest/test-conversions.cc.
doxygen¶
- Homepage:
- Spack package:
- Versions:
- 1.8.12, 1.8.11, 1.8.10
- Build Dependencies:
- cmake, bison, flex
- Run Dependencies:
- graphviz
- Description:
- Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..
dri2proto¶
- Homepage:
- Spack package:
- Versions:
- 2.8
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Direct Rendering Infrastructure 2 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.
dri3proto¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Direct Rendering Infrastructure 3 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.
dtcmp¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0, 1.0.3
- Build Dependencies:
- lwgrp, mpi
- Link Dependencies:
- lwgrp, mpi
- Description:
- The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications.
dyninst¶
- Homepage:
- Spack package:
- Versions:
- 9.3.2, 9.3.0, 9.2.0, 9.1.0, 8.2.1, 8.1.2, 8.1.1
- Build Dependencies:
- cmake, libdwarf, boost
- Link Dependencies:
- libdwarf, elf, boost
- Description:
- API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.
ea-utils¶
- Homepage:
- Spack package:
- Versions:
- 1.04.807
- Build Dependencies:
- zlib, subversion, gsl, bamtools, perl
- Link Dependencies:
- zlib, subversion, gsl, bamtools
- Description:
- Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
easybuild¶
- Homepage:
- Spack package:
- Versions:
- 3.1.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python, py-easybuild-easyblocks, py-easybuild-easyconfigs, py-easybuild-framework
- Description:
- EasyBuild is a software build and installation framework for (scientific) software on HPC systems.
ebms¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- This is a miniapp for the Energy Banding Monte Carlo (EBMC) neutron transportation simulation code. It is adapted from a similar miniapp provided by Andrew Siegel, whose algorithm is described in [1], where only one process in a compute node is used, and the compute nodes are divided into memory nodes and tracking nodes. Memory nodes do not participate in particle tracking. Obviously, there is a lot of resource waste in this design.
eccodes¶
- Homepage:
- Spack package:
- Versions:
- 2.5.0, 2.2.0
- Build Dependencies:
- netcdf, libpng, openjpeg, py-numpy, cmake, jasper, python, libaec
- Link Dependencies:
- netcdf, libpng, openjpeg, jasper, python, libaec
- Run Dependencies:
- py-numpy, python
- Description:
- ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats.
ecp-proxy-apps¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- macsio, minife, candle-benchmarks, miniamr, comd, sw4lite, xsbench, nekbone, laghos, minitri, swfft, amg
- Link Dependencies:
- macsio, minife, candle-benchmarks, miniamr, comd, sw4lite, xsbench, nekbone, laghos, minitri, swfft, amg
- Description:
- This is a collection of packages that represents the official suite of DOE/ECP proxy applications. This is a Spack bundle package that installs the ECP proxy application suite.
editres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- Dynamic resource editor for X Toolkit applications.
eigen¶
- Homepage:
- Spack package:
- Versions:
- 3.3.3, 3.3.1, 3.2.10, 3.2.9, 3.2.8, 3.2.7
- Build Dependencies:
- metis, fftw, cmake, mpfr, scotch, suite-sparse, gmp
- Link Dependencies:
- metis, fftw, mpfr, scotch, suite-sparse, gmp
- Description:
- Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.
elemental¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.87.7, 0.87.6, hydrogen-develop
- Build Dependencies:
- metis, lapack, essl, intel-mkl, mpi, cmake, gmp, openblas, veclibfort, mpfr, netlib-lapack, mpc, python, scalapack, blas
- Link Dependencies:
- metis, lapack, essl, intel-mkl, mpi, gmp, openblas, veclibfort, mpfr, netlib-lapack, mpc, python, scalapack, blas
- Description:
- Elemental: Distributed-memory dense and sparse-direct linear algebra and optimization library.
elfutils¶
- Homepage:
- Spack package:
- Versions:
- 0.170, 0.168, 0.163
- Build Dependencies:
- bison, gettext, flex
- Link Dependencies:
- gettext
- Description:
- elfutils is a collection of various binary tools such as eu-objdump, eu- readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.
elk¶
- Homepage:
- Spack package:
- Versions:
- 3.3.17
- Build Dependencies:
- lapack, libxc, fftw, blas, mpi
- Link Dependencies:
- lapack, libxc, fftw, blas, mpi
- Description:
- An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.
elpa¶
- Homepage:
- Spack package:
- Versions:
- 2017.05.003, 2017.05.002, 2016.11.001.pre, 2016.05.004, 2016.05.003, 2015.11.001
- Build Dependencies:
- lapack, scalapack, mpi, blas
- Link Dependencies:
- lapack, scalapack, mpi, blas
- Description:
- Eigenvalue solvers for Petaflop-Applications (ELPA)
emacs¶
- Homepage:
- Spack package:
- Versions:
- 25.3, 25.2, 25.1, 24.5
- Build Dependencies:
- libpng, pkgconfig, ncurses, zlib, libx11, giflib, libxpm, libxaw, libtiff, gtkplus, gnutls
- Link Dependencies:
- libpng, ncurses, zlib, libx11, giflib, libxpm, libxaw, libtiff, gtkplus, gnutls
- Description:
- The Emacs programmable text editor.
emboss¶
- Homepage:
- Spack package:
- Versions:
- 6.6.0
- Build Dependencies:
- libxpm, libgd, postgresql
- Link Dependencies:
- libxpm, libgd, postgresql
- Description:
- EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community
encodings¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, font-util, util-macros, mkfontscale
- Link Dependencies:
- font-util
- Description:
- X.org encodings font.
environment-modules¶
- Homepage:
- Spack package:
- Versions:
- 3.2.10
- Build Dependencies:
- tcl
- Link Dependencies:
- tcl
- Run Dependencies:
- tcl
- Description:
- The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles.
es¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- Es is an extensible shell. The language was derived from the Plan 9 shell, rc, and was influenced by functional programming languages, such as Scheme, and the Tcl embeddable programming language. This implementation is derived from Byron Rakitzis's public domain implementation of rc.
esmf¶
- Homepage:
- Spack package:
- Versions:
- 7.0.1
- Build Dependencies:
- netcdf, netcdf-fortran, zlib, mpi, lapack, parallel-netcdf, xerces-c, libxml2
- Link Dependencies:
- netcdf, netcdf-fortran, zlib, mpi, lapack, parallel-netcdf, xerces-c, libxml2
- Description:
- The Earth System Modeling Framework (ESMF) is high-performance, flexible software infrastructure for building and coupling weather, climate, and related Earth science applications. The ESMF defines an architecture for composing complex, coupled modeling systems and includes data structures and utilities for developing individual models.
espresso¶
- Homepage:
- Spack package:
- Versions:
- 6.1.0, 5.4.0, 5.3.0
- Build Dependencies:
- fftw, elpa, mpi, lapack, scalapack, hdf5, blas
- Link Dependencies:
- fftw, elpa, mpi, lapack, scalapack, hdf5, blas
- Description:
- Quantum-ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
essl¶
- Homepage:
- Spack package:
- Versions:
- 5.5
- Description:
- IBM's Engineering and Scientific Subroutine Library (ESSL).
ethminer¶
- Homepage:
- Spack package:
- Versions:
- 0.12.0
- Build Dependencies:
- cuda, json-c, zlib, boost, python, curl, cmake, mesa
- Link Dependencies:
- cuda, json-c, zlib, boost, curl, python, mesa
- Description:
- The ethminer is an Ethereum GPU mining worker.
etsf-io¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- netcdf-fortran, hdf5
- Link Dependencies:
- netcdf-fortran, hdf5
- Description:
- ETSF_IO is a library implementing the Nanoquanta/ETSF file format specifications. ETSF_IO enables an architecture-independent exchange of crystallographic data, electronic wavefunctions, densities and potentials, as well as spectroscopic data. It is meant to be used by quantum-physical and quantum-chemical applications relying upon Density Functional Theory (DFT).
everytrace¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.2.0
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- Get stack trace EVERY time a program exits.
everytrace-example¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, openmpi, everytrace
- Link Dependencies:
- openmpi, everytrace
- Description:
- Get stack trace EVERY time a program exits.
evieext¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Extended Visual Information Extension (XEVIE). This extension defines a protocol for a client to determine information about core X visuals beyond what the core protocol provides.
exabayes¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.
exampm¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake
- Description:
- Exascale Material Point Method (MPM) Mini-App
exasp2¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- lapack, blas, bml, mpi
- Link Dependencies:
- lapack, blas, bml, mpi
- Description:
- ExaSP2 is a reference implementation of typical linear algebra algorithms and workloads for a quantum molecular dynamics (QMD) electronic structure code. The algorithm is based on a recursive second- order Fermi-Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of material systems. The SP2 algorithm variants are part of the Los Alamos Transferable Tight-binding for Energetics (LATTE) code, based on a matrix expansion of the Fermi operator in a recursive series of generalized matrix-matrix multiplications. It is created and maintained by Co-Design Center for Particle Applications (CoPA). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement as needed to test performance of new architectures, programming models, etc.
exmcutils¶
- Homepage:
- Spack package:
- Versions:
- 0.5.3
- Description:
- ExM C-Utils: Generic C utility library for ADLB/X and Swift/T
exodusii¶
- Homepage:
- Spack package:
- Versions:
- 2016-08-09
- Build Dependencies:
- netcdf, hdf5, cmake, mpi
- Link Dependencies:
- netcdf, hdf5, mpi
- Description:
- Exodus II is a C++/Fortran library developed to store and retrieve data for finite element analyses. It's used for preprocessing (problem definition), postprocessing (results visualization), and data transfer between codes. An Exodus II data file is a random access, machine independent, binary file that is written and read via C, C++, or Fortran API routines.
exonerate¶
- Homepage:
- Spack package:
- Versions:
- 2.4.0
- Build Dependencies:
- pkgconfig, glib
- Link Dependencies:
- glib
- Description:
- Pairwise sequence alignment of DNA and proteins
expat¶
- Homepage:
- Spack package:
- Versions:
- 2.2.2, 2.2.0
- Build Dependencies:
- libbsd
- Link Dependencies:
- libbsd
- Description:
- Expat is an XML parser library written in C.
expect¶
- Homepage:
- Spack package:
- Versions:
- 5.45
- Build Dependencies:
- tcl, autoconf, m4, libtool, automake
- Link Dependencies:
- tcl
- Description:
- Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.
express¶
- Homepage:
- Spack package:
- Versions:
- 2015-11-29
- Build Dependencies:
- cmake, zlib, boost, bamtools
- Link Dependencies:
- zlib, boost, bamtools
- Description:
- eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
extrae¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1
- Build Dependencies:
- papi, libunwind, libdwarf, gettext, mpi, dyninst, binutils, boost, libxml2
- Link Dependencies:
- papi, libunwind, boost, libdwarf, gettext, mpi, dyninst, binutils, elf, libxml2
- Description:
- Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance. The Extrae instrumentation package can instrument the MPI programin model, and the following parallel programming models either alone or in conjunction with MPI : OpenMP, CUDA, OpenCL, pthread, OmpSs
f90cache¶
- Homepage:
- Spack package:
- Versions:
- 0.99
- Description:
- f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.
falcon¶
- Homepage:
- Spack package:
- Versions:
- 2017-05-30
- Build Dependencies:
- python, py-networkx
- Link Dependencies:
- python
- Run Dependencies:
- py-pypeflow, pacbio-daligner, py-networkx, pacbio-dazz-db, pacbio-damasker, pacbio-dextractor, python, py-setuptools
- Description:
- Falcon: a set of tools for fast aligning long reads for consensus and assembly. The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.
farmhash¶
- Homepage:
- Spack package:
- Versions:
- 92e897
- Build Dependencies:
- cmake
- Description:
- FarmHash provides hash functions for strings and other data.
fastjar¶
- Homepage:
- Spack package:
- Versions:
- 0.98
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Fastjar is a version of Sun's 'jar' utility, written entirely in C.
fastmath¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- hypre, pumi, phasta, sundials, mesquite, mpi, moab, boxlib, arpack-ng, trilinos, petsc, superlu-dist, chombo, zoltan
- Link Dependencies:
- hypre, pumi, phasta, sundials, mesquite, mpi, moab, boxlib, arpack-ng, trilinos, petsc, superlu-dist, chombo, zoltan
- Description:
- FASTMath is a suite of ~15 numerical libraries frequently used together in various SciDAC and CSE applications. The suite includes discretization libraries for structured, AMR and unstructured grids as well as solver libraries for ODE's, Time Integrators, Iterative, Non- Linear, and Direct Solvers.
fastme¶
- Homepage:
- Spack package:
- Versions:
- 2.1.5.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.
fastphase¶
- Homepage:
- Spack package:
- Versions:
- 2016-03-30
- Description:
- Software for haplotype reconstruction, and estimating missing genotypes from population data.
fastq-screen¶
- Homepage:
- Spack package:
- Versions:
- 0.11.2
- Build Dependencies:
- bowtie2, samtools, bwa, bowtie
- Link Dependencies:
- bowtie2, samtools, bwa, bowtie
- Run Dependencies:
- perl, perl-gd-graph
- Description:
- FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
fastqc¶
- Homepage:
- Spack package:
- Versions:
- 0.11.5, 0.11.4
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- java
- Description:
- A quality control tool for high throughput sequence data.
fastqvalidator¶
- Homepage:
- Spack package:
- Versions:
- 2017-01-10
- Description:
- The fastQValidator validates the format of fastq files.
fasttree¶
- Homepage:
- Spack package:
- Versions:
- 2.1.10
- Description:
- FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
fastx-toolkit¶
- Homepage:
- Spack package:
- Versions:
- 0.0.14
- Build Dependencies:
- libgtextutils
- Link Dependencies:
- libgtextutils
- Description:
- The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fenics¶
- Homepage:
- Spack package:
- Versions:
- 2016.1.0, 1.6.0, 1.5.0
- Build Dependencies:
- py-numpy, hdf5, cmake, parmetis, py-setuptools, qt, mpi, suite-sparse, py-sympy, slepc, trilinos, petsc, boost, py-sphinx, scotch, swig, eigen, py-ply, python, py-six, vtk
- Link Dependencies:
- hdf5, parmetis, scotch, qt, suite-sparse, slepc, trilinos, petsc, boost, mpi, eigen, python, vtk
- Run Dependencies:
- py-numpy, swig, py-ply, py-six, py-sympy
- Description:
- FEniCS is organized as a collection of interoperable components that together form the FEniCS Project. These components include the problem- solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.
ferret¶
- Homepage:
- Spack package:
- Versions:
- 6.96
- Build Dependencies:
- netcdf, hdf5, zlib, readline, netcdf-fortran
- Link Dependencies:
- netcdf, hdf5, zlib, readline, netcdf-fortran
- Description:
- Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.
ffmpeg¶
- Homepage:
- Spack package:
- Versions:
- 3.2.4
- Build Dependencies:
- yasm
- Link Dependencies:
- yasm
- Description:
- FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.
fftw¶
- Homepage:
- Spack package:
- Versions:
- 3.3.7, 3.3.6-pl2, 3.3.5, 3.3.4, 2.1.5
- Build Dependencies:
- automake, autoconf, libtool, mpi
- Link Dependencies:
- mpi
- Description:
- FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.
fimpute¶
- Homepage:
- Spack package:
- Versions:
- 2014-01
- Description:
- FImpute uses an overlapping sliding window approach to efficiently exploit relationships or haplotype similarities between target and reference individuals.
findutils¶
- Homepage:
- Spack package:
- Versions:
- 4.6.0, 4.4.2, 4.4.1, 4.4.0, 4.2.33, 4.2.32, 4.2.31, 4.2.30, 4.2.29, 4.2.28, 4.2.27, 4.2.26, 4.2.25, 4.2.23, 4.2.20, 4.2.18, 4.2.15, 4.1.20, 4.1
- Description:
- The GNU Find Utilities are the basic directory searching utilities of the GNU operating system.
fio¶
- Homepage:
- Spack package:
- Versions:
- 2.19
- Build Dependencies:
- gtkplus, cairo, py-sphinx
- Link Dependencies:
- gtkplus, cairo
- Description:
- Flexible I/O Tester.
fish¶
- Homepage:
- Spack package:
- Versions:
- 2.7.1, 2.7.0, 2.2.0
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.
fixesproto¶
- Homepage:
- Spack package:
- Versions:
- 5.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Fixes Extension. The extension makes changes to many areas of the protocol to resolve issues raised by application interaction with core protocol mechanisms that cannot be adequately worked around on the client side of the wire.
flac¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2, 1.3.1, 1.3.0
- Build Dependencies:
- libvorbis, id3lib
- Link Dependencies:
- libvorbis, id3lib
- Description:
- Encoder/decoder for the Free Lossless Audio Codec
flang¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- llvm, cmake
- Link Dependencies:
- llvm
- Description:
- Flang is a Fortran compiler targeting LLVM.
flann¶
- Homepage:
- Spack package:
- Versions:
- 1.9.1, 1.8.5, 1.8.4, 1.8.1, 1.8.0
- Build Dependencies:
- py-numpy, cuda, hdf5, boost, matlab, python, mpi, cmake, latex
- Link Dependencies:
- cuda, latex, hdf5, boost, mpi, python
- Run Dependencies:
- py-numpy, matlab
- Description:
- FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. It contains a collection of algorithms we found to work best for nearest neighbor search and a system for automatically choosing the best algorithm and optimum parameters depending on the dataset. FLANN is written in C++ and contains bindings for the following languages: C, MATLAB and Python.
flash¶
- Homepage:
- Spack package:
- Versions:
- 1.2.11
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.
flecsale¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- flecsi, cmake, python, openssl
- Link Dependencies:
- flecsi, openssl, python
- Description:
- Flecsale is an ALE code based on FleCSI
flecsi¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, legion
- Link Dependencies:
- legion
- Description:
- FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces,and dependency closures.
flex¶
- Homepage:
- Spack package:
- Versions:
- 2.6.4, 2.6.3, 2.6.1, 2.6.0, 2.5.39
- Build Dependencies:
- autoconf, m4, libtool, gettext, automake, bison, help2man
- Description:
- Flex is a tool for generating scanners.
flint¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.5.2, 2.4.5
- Build Dependencies:
- autoconf, gmp, mpfr
- Link Dependencies:
- gmp, mpfr
- Description:
- FLINT (Fast Library for Number Theory).
flit¶
- Homepage:
- Spack package:
- Versions:
- 2.0-alpha.1
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-toml
- Description:
- Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for detecting variability in floating-point code caused by variations in compiler code generation, hardware and execution environments.
fltk¶
- Homepage:
- Spack package:
- Versions:
- 1.3.3
- Build Dependencies:
- libx11
- Link Dependencies:
- libx11
- Description:
- FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK also includes an excellent UI builder called FLUID that can be used to create applications in minutes.
flux¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0, master
- Build Dependencies:
- munge, py-cffi, zeromq, libtool, automake, hwloc, asciidoc, czmq, autoconf, jansson, lua-luaposix, lua, python, libuuid
- Link Dependencies:
- munge, czmq, zeromq, jansson, lua-luaposix, python, lua, hwloc, libuuid
- Run Dependencies:
- py-cffi
- Description:
- A next-generation resource manager (pre-alpha)
fmt¶
- Homepage:
- Spack package:
- Versions:
- 4.0.0, 3.0.2, 3.0.1, 3.0.0
- Build Dependencies:
- cmake
- Description:
- fmt (formerly cppformat) is an open-source formatting library. It can be used as a safe alternative to printf or as a fast alternative to C++ IOStreams.
foam-extend¶
- Homepage:
- Spack package:
- Versions:
- 4.0, 3.2, 3.1, 3.0
- Build Dependencies:
- metis, python, zlib, parmgridgen, flex, paraview, scotch, parmetis, cmake, mpi
- Link Dependencies:
- metis, zlib, mpi, paraview, scotch, parmetis, python
- Description:
- The Extend Project is a fork of the OpenFOAM opensource library for Computational Fluid Dynamics (CFD). This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.
folly¶
- Homepage:
- Spack package:
- Versions:
- 2017.06.05.00, 2016.11.14.00, 2016.11.07.00, 2016.10.31.00, 2016.10.24.00, 2016.10.17.00
- Build Dependencies:
- double-conversion, autoconf, m4, libtool, glog, pkgconfig, automake, libevent, gflags, boost
- Link Dependencies:
- boost, libevent, glog, double-conversion, gflags
- Description:
- Folly (acronymed loosely after Facebook Open Source Library) is a library of C++11 components designed with practicality and efficiency in mind. Folly contains a variety of core library components used extensively at Facebook. In particular, it's often a dependency of Facebook's other open source C++ efforts and place where those projects can share code.
font-adobe-100dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org adobe-100dpi font.
font-adobe-75dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org adobe-75dpi font.
font-adobe-utopia-100dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org adobe-utopia-100dpi font.
font-adobe-utopia-75dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org adobe-utopia-75dpi font.
font-adobe-utopia-type1¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Description:
- X.org adobe-utopia-type1 font.
font-alias¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- pkgconfig, font-util, util-macros
- Link Dependencies:
- font-util
- Description:
- X.org alias font.
font-arabic-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org arabic-misc font.
font-bh-100dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-100dpi font.
font-bh-75dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-75dpi font.
font-bh-lucidatypewriter-100dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-lucidatypewriter-100dpi font.
font-bh-lucidatypewriter-75dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-lucidatypewriter-75dpi font.
font-bh-ttf¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-ttf font.
font-bh-type1¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bh-type1 font.
font-bitstream-100dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bitstream-100dpi font.
font-bitstream-75dpi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bitstream-75dpi font.
font-bitstream-speedo¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bitstream-speedo font.
font-bitstream-type1¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org bitstream-type1 font.
font-cronyx-cyrillic¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org cronyx-cyrillic font.
font-cursor-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org cursor-misc font.
font-daewoo-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org daewoo-misc font.
font-dec-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org dec-misc font.
font-ibm-type1¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org ibm-type1 font.
font-isas-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org isas-misc font.
font-jis-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org jis-misc font.
font-micro-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org micro-misc font.
font-misc-cyrillic¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org misc-cyrillic font.
font-misc-ethiopic¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org misc-ethiopic font.
font-misc-meltho¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org misc-meltho font.
font-misc-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org misc-misc font.
font-mutt-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org mutt-misc font.
font-schumacher-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org schumacher-misc font.
font-screen-cyrillic¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org screen-cyrillic font.
font-sony-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org sony-misc font.
font-sun-misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org sun-misc font.
font-util¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X.Org font package creation/installation utilities.
font-winitzki-cyrillic¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- fontconfig, bdftopcf, util-macros, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org winitzki-cyrillic font.
font-xfree86-type1¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- fontconfig, util-macros, mkfontscale, pkgconfig, font-util, mkfontdir
- Link Dependencies:
- font-util
- Description:
- X.org xfree86-type1 font.
fontcacheproto¶
- Homepage:
- Spack package:
- Versions:
- 0.1.3
- Description:
- X.org FontcacheProto protocol headers.
fontconfig¶
- Homepage:
- Spack package:
- Versions:
- 2.12.3, 2.12.1, 2.11.1
- Build Dependencies:
- pkgconfig, font-util, gperf, freetype, libxml2
- Link Dependencies:
- font-util, freetype, libxml2
- Description:
- Fontconfig is a library for configuring/customizing font access
fontsproto¶
- Homepage:
- Spack package:
- Versions:
- 2.1.3
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Fonts Extension.
fonttosfnt¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libfontenc, freetype, util-macros
- Link Dependencies:
- libfontenc, freetype
- Description:
- Wrap a bitmap font in a sfnt (TrueType) wrapper.
fpc¶
- Homepage:
- Spack package:
- Versions:
- 3.0.2
- Description:
- Free Pascal is a 32, 64 and 16 bit professional Pascal compiler.
fr-hit¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1-2013-02-20
- Build Dependencies:
- perl, python
- Link Dependencies:
- perl, python
- Description:
- An efficient algorithm for fragment recruitment for next generation sequences against microbial reference genomes.
freebayes¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- cmake, zlib
- Link Dependencies:
- zlib
- Description:
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.
freetype¶
- Homepage:
- Spack package:
- Versions:
- 2.7.1, 2.7, 2.5.3
- Build Dependencies:
- libpng, pkgconfig, bzip2
- Link Dependencies:
- libpng, bzip2
- Description:
- FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.
fseq¶
- Homepage:
- Spack package:
- Versions:
- 1.84
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags
fsl¶
- Homepage:
- Spack package:
- Versions:
- 5.0.10
- Build Dependencies:
- libpng, python, zlib, libx11, sqlite, expat, mesa-glu, boost
- Link Dependencies:
- libpng, zlib, libx11, sqlite, expat, mesa-glu, boost
- Run Dependencies:
- python
- Description:
- FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Note: A manual download is required for FSL. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
fslsfonts¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, libfs, util-macros, xproto
- Link Dependencies:
- libfs
- Description:
- fslsfonts produces a list of fonts served by an X font server.
fstobdf¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- pkgconfig, libfs, libx11, util-macros, xproto
- Link Dependencies:
- libfs, libx11
- Description:
- The fstobdf program reads a font from a font server and prints a BDF file on the standard output that may be used to recreate the font. This is useful in testing servers, debugging font metrics, and reproducing lost BDF files.
funhpc¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.3.0, 1.2.0, 1.1.1, 1.1.0, 1.0.0, 0.1.1, 0.1.0
- Build Dependencies:
- cereal, qthreads, mpi, hwloc, cmake, googletest, jemalloc
- Link Dependencies:
- cereal, qthreads, mpi, hwloc, googletest, jemalloc
- Description:
- FunHPC: Functional HPC Programming
gapbs¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Description:
- The GAP Benchmark Suite is intended to help graph processing research by standardizing evaluations. Fewer differences between graph processing evaluations will make it easier to compare different research efforts and quantify improvements. The benchmark not only specifies graph kernels, input graphs, and evaluation methodologies, but it also provides an optimized baseline implementation (this repo). These baseline implementations are representative of state-of-the-art performance, and thus new contributions should outperform them to demonstrate an improvement.
gapcloser¶
- Homepage:
- Spack package:
- Versions:
- 1.12-r6
- Description:
- The GapCloser is designed to close the gaps emerging during the scaffolding process
gapfiller¶
- Homepage:
- Spack package:
- Versions:
- 1.10
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. Note: A manual download is required for GapFiller. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
gasnet¶
- Homepage:
- Spack package:
- Versions:
- 1.30.0, 1.28.2, 1.28.0, 1.24.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries such as UPC, Co-Array Fortran, SHMEM, Cray Chapel, and Titanium.
gatk¶
- Homepage:
- Spack package:
- Versions:
- 3.8-0
- Run Dependencies:
- java
- Description:
- Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data
gaussian¶
- Homepage:
- Spack package:
- Versions:
- 09
- Description:
- Gaussian is a computer program for computational chemistry
gawk¶
- Homepage:
- Spack package:
- Versions:
- 4.1.4
- Build Dependencies:
- libsigsegv, mpfr, gettext, readline, gmp
- Link Dependencies:
- libsigsegv, mpfr, gettext, readline, gmp
- Description:
- If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time- consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
gblocks¶
- Homepage:
- Spack package:
- Versions:
- 0.91b
- Description:
- Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
gcc¶
- Homepage:
- Spack package:
- Versions:
- 7.3.0, 7.2.0, 7.1.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4
- Build Dependencies:
- gnat, binutils, mpc, isl, zip, mpfr, zlib, gmp
- Link Dependencies:
- gnat, mpc, mpfr, isl, binutils, zlib, gmp
- Description:
- The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.
gccmakedep¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- pkgconfig
- Description:
- X.org gccmakedep utilities.
gccxml¶
- Homepage:
- Spack package:
- Versions:
- develop, latest
- Build Dependencies:
- cmake
- Description:
- gccxml dumps an XML description of C++ source code using an extension of the GCC C++ compiler.
gconf¶
- Homepage:
- Spack package:
- Versions:
- 3.2.6
- Build Dependencies:
- glib, libxml2
- Link Dependencies:
- glib, libxml2
- Description:
- GConf is a system for storing application preferences.
gdal¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2, 2.0.2
- Build Dependencies:
- netcdf, libpng, openjpeg, hdf5, kealib, geos, zlib, py-numpy, proj, hdf, swig, libtiff, python
- Link Dependencies:
- netcdf, libpng, openjpeg, hdf5, kealib, geos, zlib, proj, hdf, swig, libtiff, python
- Run Dependencies:
- py-numpy
- Description:
- GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.
gdb¶
- Homepage:
- Spack package:
- Versions:
- 8.0.1, 8.0, 7.12.1, 7.11, 7.10.1, 7.10, 7.9.1, 7.9, 7.8.2
- Build Dependencies:
- python, texinfo
- Link Dependencies:
- python
- Description:
- GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed.
gdbm¶
- Homepage:
- Spack package:
- Versions:
- 1.14.1, 1.13, 1.12, 1.11, 1.10, 1.9.1, 1.9
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.
gdk-pixbuf¶
- Homepage:
- Spack package:
- Versions:
- 2.31.2
- Build Dependencies:
- libpng, gettext, pkgconfig, libtiff, gobject-introspection, glib, jpeg
- Link Dependencies:
- libpng, gettext, libtiff, gobject-introspection, glib, jpeg
- Description:
- The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
geant4¶
- Homepage:
- Spack package:
- Versions:
- 10.04, 10.03.p03, 10.02.p03, 10.02.p02, 10.02.p01, 10.01.p03
- Build Dependencies:
- zlib, libx11, clhep, mesa, expat, qt, motif, cmake, libxmu, xerces-c, vecgeom
- Link Dependencies:
- zlib, libx11, clhep, mesa, expat, qt, motif, libxmu, xerces-c, vecgeom
- Description:
- Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
gearshifft¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1-lw
- Build Dependencies:
- cuda, clfft, fftw, boost, cmake, opencl
- Link Dependencies:
- cuda, clfft, fftw, boost, opencl
- Description:
- Benchmark Suite for Heterogenuous FFT Implementations
gemmlowp¶
- Homepage:
- Spack package:
- Versions:
- a6f29d9ac
- Description:
- Google low-precision matrix multiplication library
genemark-et¶
- Homepage:
- Spack package:
- Versions:
- 4.33
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes.
genometools¶
- Homepage:
- Spack package:
- Versions:
- 1.5.9
- Build Dependencies:
- perl, cairo, pango
- Link Dependencies:
- cairo, pango
- Run Dependencies:
- perl
- Description:
- genometools is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.
geos¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0, 3.4.2, 3.4.1, 3.4.0, 3.3.9, 3.3.8, 3.3.7, 3.3.6, 3.3.5, 3.3.4, 3.3.3
- Description:
- GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.
gettext¶
- Homepage:
- Spack package:
- Versions:
- 0.19.8.1, 0.19.7
- Build Dependencies:
- libunistring, ncurses, xz, bzip2, tar, libxml2
- Link Dependencies:
- libunistring, ncurses, xz, bzip2, tar, libxml2
- Description:
- GNU internationalization (i18n) and localization (l10n) library.
gflags¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2
- Build Dependencies:
- cmake
- Description:
- The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Online documentation available at: https://gflags.github.io/gflags/
ghostscript¶
- Homepage:
- Spack package:
- Versions:
- 9.21, 9.18
- Build Dependencies:
- libpng, libxext, freetype, lcms, pkgconfig, zlib, libtiff, jpeg
- Link Dependencies:
- libpng, libxext, freetype, lcms, zlib, libtiff, jpeg
- Description:
- An interpreter for the PostScript language and for PDF.
giflib¶
- Homepage:
- Spack package:
- Versions:
- 5.1.4
- Description:
- The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989.
git¶
- Homepage:
- Spack package:
- Versions:
- 2.15.1, 2.14.1, 2.13.0, 2.12.2, 2.12.1, 2.12.0, 2.11.1, 2.11.0, 2.9.3, 2.9.2, 2.9.1, 2.9.0, 2.8.4, 2.8.3, 2.8.2, 2.8.1, 2.8.0, 2.7.3, 2.7.1
- Build Dependencies:
- zlib, libtool, gettext, automake, curl, pcre, perl, autoconf, m4, openssl, libiconv, expat
- Link Dependencies:
- perl, zlib, gettext, libiconv, openssl, curl, pcre, expat
- Description:
- Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
git-lfs¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0, 2.2.1, 2.0.2, 1.4.1, 1.3.1
- Build Dependencies:
- go
- Run Dependencies:
- git
- Description:
- Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special "pointer files" in the repository, while storing the actual file contents on a Git LFS server.
gl2ps¶
- Homepage:
- Spack package:
- Versions:
- 1.3.9
- Build Dependencies:
- libdrm, libxdamage, zlib, libxt, libxfixes, libxmu, cmake, libxxf86vm, libpng, libice, libxext, libsm, libxau, libxdmcp, expat, libxcb, libxi
- Link Dependencies:
- libdrm, libxdamage, zlib, libxt, libxfixes, libxmu, libxxf86vm, libpng, libice, libxext, libsm, libxau, libxdmcp, expat, libxcb, libxi
- Description:
- GL2PS is a C library providing high quality vector output for any OpenGL application.
glew¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0
- Build Dependencies:
- cmake
- Description:
- The OpenGL Extension Wrangler Library.
glib¶
- Homepage:
- Spack package:
- Versions:
- 2.55.1, 2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
- Build Dependencies:
- perl, python, zlib, gettext, util-linux, pkgconfig, libffi, pcre
- Link Dependencies:
- libffi, util-linux, pcre, zlib, gettext
- Run Dependencies:
- perl, python
- Description:
- The GLib package contains a low-level libraries useful for providing data structure handling for C, portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system.
glm¶
- Homepage:
- Spack package:
- Versions:
- 0.9.7.1
- Build Dependencies:
- cmake
- Description:
- OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specification
global¶
- Homepage:
- Spack package:
- Versions:
- 6.5
- Build Dependencies:
- exuberant-ctags, ncurses
- Link Dependencies:
- ncurses
- Run Dependencies:
- exuberant-ctags
- Description:
- The Gnu Global tagging system
globalarrays¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- lapack, blas, cmake, mpi
- Link Dependencies:
- lapack, blas, mpi
- Description:
- The Global Arrays (GA) toolkit provides a shared memory style programming environment in the context of distributed array data structures.
globus-toolkit¶
- Homepage:
- Spack package:
- Versions:
- 6.0.1506371041, 6.0.1493989444
- Build Dependencies:
- openssl
- Link Dependencies:
- openssl
- Description:
- The Globus Toolkit is an open source software toolkit used for building grids
glog¶
- Homepage:
- Spack package:
- Versions:
- 0.3.5, 0.3.4, 0.3.3
- Build Dependencies:
- cmake, gflags
- Link Dependencies:
- cmake, gflags
- Description:
- C++ implementation of the Google logging module.
glpk¶
- Homepage:
- Spack package:
- Versions:
- 4.61, 4.57
- Build Dependencies:
- gmp
- Link Dependencies:
- gmp
- Description:
- The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
glproto¶
- Homepage:
- Spack package:
- Versions:
- 1.4.17
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- OpenGL Extension to the X Window System. This extension defines a protocol for the client to send 3D rendering commands to the X server.
gmake¶
- Homepage:
- Spack package:
- Versions:
- 4.2.1, 4.0
- Build Dependencies:
- guile
- Link Dependencies:
- guile
- Description:
- GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.
gmap-gsnap¶
- Homepage:
- Spack package:
- Versions:
- 2017-06-16, 2014-12-28
- Description:
- GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program
gmime¶
- Homepage:
- Spack package:
- Versions:
- 2.6.23
- Build Dependencies:
- glib, libgpg-error
- Link Dependencies:
- glib, libgpg-error
- Description:
- GMime is a C/C++ library which may be used for the creation and parsing of messages using the Multipurpose Internet Mail Extension (MIME).
gmp¶
- Homepage:
- Spack package:
- Versions:
- 6.1.2, 6.1.1, 6.1.0, 6.0.0a, 6.0.0
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.
gmsh¶
- Homepage:
- Spack package:
- Versions:
- 3.0.6, 3.0.1, 2.16.0, 2.15.0, 2.12.0, 2.11.0
- Build Dependencies:
- slepc, hdf5, fltk, oce, mpi, lapack, petsc, gmp, cmake, zlib, blas
- Link Dependencies:
- slepc, hdf5, fltk, oce, mpi, lapack, petsc, gmp, zlib, blas
- Description:
- Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.
gnat¶
- Homepage:
- Spack package:
- Versions:
- 2016
- Description:
- The GNAT Ada compiler. Ada is a modern programming language designed for large, long-lived applications - and embedded systems in particular - where reliability and efficiency are essential.
gnu-prolog¶
- Homepage:
- Spack package:
- Versions:
- 1.4.4
- Description:
- A free Prolog compiler with constraint solving over finite domains.
gnupg¶
- Homepage:
- Spack package:
- Versions:
- 2.2.3, 2.1.21
- Build Dependencies:
- npth, libgcrypt, libassuan, libksba, libgpg-error
- Link Dependencies:
- npth, libgcrypt, libassuan, libksba, libgpg-error
- Description:
- GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880
gnuplot¶
- Homepage:
- Spack package:
- Versions:
- 5.2.0, 5.0.7, 5.0.6, 5.0.5, 5.0.1
- Build Dependencies:
- pkgconfig, libcerf, wx, cairo, libiconv, libxpm, libgd, pango, readline
- Link Dependencies:
- libcerf, wx, cairo, libiconv, libxpm, libgd, pango, readline
- Description:
- Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986
gnutls¶
- Homepage:
- Spack package:
- Versions:
- 3.5.13, 3.5.10, 3.5.9, 3.3.9
- Build Dependencies:
- pkgconfig, nettle, zlib, gettext
- Link Dependencies:
- nettle, zlib, gettext
- Description:
- GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.
go¶
- Homepage:
- Spack package:
- Versions:
- 1.9.2, 1.9.1, 1.9, 1.8.3, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.6.4
- Build Dependencies:
- go-bootstrap, git
- Link Dependencies:
- git
- Run Dependencies:
- git
- Description:
- The golang compiler and build environment
go-bootstrap¶
- Homepage:
- Spack package:
- Versions:
- 1.4-bootstrap-20170531, 1.4-bootstrap-20161024
- Build Dependencies:
- git
- Link Dependencies:
- git
- Run Dependencies:
- git
- Description:
- Old C-bootstrapped go to bootstrap real go
gobject-introspection¶
- Homepage:
- Spack package:
- Versions:
- 1.49.2, 1.48.0
- Build Dependencies:
- cairo, flex, pkgconfig, python, bison, glib, sed
- Link Dependencies:
- python, cairo, glib
- Description:
- The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output
googletest¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0, 1.7.0, 1.6.0
- Build Dependencies:
- cmake
- Description:
- Google test framework for C++. Also called gtest.
gotcha¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.0.2, master
- Build Dependencies:
- cmake
- Description:
- C software library for shared library function wrapping, enables tools to intercept calls into shared libraries
gource¶
- Homepage:
- Spack package:
- Versions:
- 0.44
- Build Dependencies:
- libpng, glew, libtool, pkgconfig, automake, pcre, jpeg, sdl2, autoconf, sdl2-image, freetype, boost, glm
- Link Dependencies:
- libpng, sdl2, sdl2-image, freetype, boost, glew, pcre, jpeg
- Description:
- Software version control visualization.
gperf¶
- Homepage:
- Spack package:
- Versions:
- 3.0.4
- Description:
- GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
gperftools¶
- Homepage:
- Spack package:
- Versions:
- 2.4, 2.3
- Build Dependencies:
- libunwind
- Link Dependencies:
- libunwind
- Description:
- Google's fast malloc/free implementation, especially for multi-threaded applications. Contains tcmalloc, heap-checker, heap-profiler, and cpu- profiler.
grackle¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.2, 2.0.1
- Build Dependencies:
- hdf5, libtool, mpi
- Link Dependencies:
- hdf5, libtool, mpi
- Description:
- Grackle is a chemistry and radiative cooling library for astrophysical simulations with interfaces for C, C++, and Fortran codes. It is a generalized and trimmed down version of the chemistry network of the Enzo simulation code
gradle¶
- Homepage:
- Spack package:
- Versions:
- 3.4, 3.3, 3.2.1, 3.2, 3.1, 3.0, 2.14.1, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2.1, 2.2, 2.1, 2.0, 1.12, 1.11, 1.10, 1.9, 1.8, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0, 0.9.2, 0.9.1, 0.9, 0.8, 0.7
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Gradle is an open source build automation system that builds upon the concepts of Apache Ant and Apache Maven and introduces a Groovy-based domain-specific language (DSL) instead of the XML form used by Apache Maven for declaring the project configuration. Gradle uses a directed acyclic graph ("DAG") to determine the order in which tasks can be run.
grandr¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- gtkplus, xrandr, gconf
- Link Dependencies:
- gtkplus, xrandr, gconf
- Description:
- RandR user interface using GTK+ libraries.
graphlib¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.0.0
- Build Dependencies:
- cmake
- Description:
- Library to create, manipulate, and export graphs Graphlib.
graphmap¶
- Homepage:
- Spack package:
- Versions:
- 0.3.0
- Description:
- A highly sensitive and accurate mapper for long, error-prone reads
graphviz¶
- Homepage:
- Spack package:
- Versions:
- 2.40.1
- Build Dependencies:
- libpng, zlib, libtool, flex, qt, bison, glib, autoconf, freetype, gts, swig, expat, ghostscript, pkg-config, automake, fontconfig, gtkplus, java, cairo, pango, libgd, python
- Link Dependencies:
- libpng, zlib, java, cairo, qt, glib, fontconfig, gtkplus, freetype, gts, pango, expat, libgd, python, ghostscript
- Description:
- Graph Visualization Software
grib-api¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0, 1.21.0, 1.17.0, 1.16.0
- Build Dependencies:
- netcdf, libpng, openjpeg, py-numpy, cmake, jasper, python, libaec
- Link Dependencies:
- netcdf, libpng, openjpeg, jasper, python, libaec
- Run Dependencies:
- py-numpy, python
- Description:
- The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages.
groff¶
- Homepage:
- Spack package:
- Versions:
- 1.22.3
- Build Dependencies:
- gawk, ghostscript, gmake, sed
- Link Dependencies:
- ghostscript
- Description:
- Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal.
gromacs¶
- Homepage:
- Spack package:
- Versions:
- develop, 2016.4, 2016.3, 5.1.4, 5.1.2
- Build Dependencies:
- cuda, plumed, fftw, cmake, mpi
- Link Dependencies:
- cuda, plumed, fftw, mpi
- Description:
- GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.
gsl¶
- Homepage:
- Spack package:
- Versions:
- 2.4, 2.3, 2.2.1, 2.1, 2.0, 1.16
- Description:
- The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
gslib¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0.0
- Build Dependencies:
- mpi, blas
- Link Dependencies:
- mpi, blas
- Description:
- Highly scalable Gather-scatter code with AMG and XXT solvers
gtkorvo-atl¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1
- Build Dependencies:
- cmake, gtkorvo-cercs-env
- Link Dependencies:
- gtkorvo-cercs-env
- Description:
- Libatl provides a library for the creation and manipulation of lists of name/value pairs using an efficient binary representation.
gtkorvo-cercs-env¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- cmake
- Description:
- A utility library used by some GTkorvo packages.
gtkorvo-dill¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1
- Build Dependencies:
- cmake
- Description:
- DILL provides instruction-level code generation, register allocation and simple optimizations for generating executable code directly into memory regions for immediate use.
gtkorvo-enet¶
- Homepage:
- Spack package:
- Versions:
- 1.3.13
- Description:
- ENet reliable UDP networking library. This is a downstream branch of lsalzman's ENet. This version has expanded the client ID to handle more clients. The original is at http://github.com/lsalzman/enet.
gtkplus¶
- Homepage:
- Spack package:
- Versions:
- 2.24.32, 2.24.31, 2.24.25
- Build Dependencies:
- atk, pango, pkgconfig, gobject-introspection, glib, gdk-pixbuf, shared-mime-info
- Link Dependencies:
- atk, pango, gobject-introspection, glib, gdk-pixbuf, shared-mime-info
- Description:
- The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
gts¶
- Homepage:
- Spack package:
- Versions:
- 121130
- Build Dependencies:
- glib
- Link Dependencies:
- glib
- Description:
- GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. The source code is available free of charge under the Free Software LGPL license. The code is written entirely in C with an object-oriented approach based mostly on the design of GTK+. Careful attention is paid to performance related issues as the initial goal of GTS is to provide a simple and efficient library to scientists dealing with 3D computational surface meshes.
guidance¶
- Homepage:
- Spack package:
- Versions:
- 2.02
- Build Dependencies:
- perl, mafft, ruby, clustalw, prank, muscle, perl-bio-perl
- Link Dependencies:
- prank, clustalw, mafft, ruby, muscle
- Run Dependencies:
- perl, perl-bio-perl
- Description:
- Guidance: Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
guile¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.0.14, 2.0.11
- Build Dependencies:
- libunistring, libffi, libtool, gettext, pkgconfig, bdw-gc, readline, gmp
- Link Dependencies:
- libunistring, libffi, libtool, gettext, bdw-gc, readline, gmp
- Description:
- Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
h5hut¶
- Homepage:
- Spack package:
- Versions:
- 1.99.13
- Build Dependencies:
- hdf5, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- H5hut (HDF5 Utility Toolkit). High-Performance I/O Library for Particle- based Simulations.
h5part¶
- Homepage:
- Spack package:
- Versions:
- 1.6.6
- Build Dependencies:
- hdf5, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- Portable High Performance Parallel Data Interface to HDF5
h5utils¶
- Homepage:
- Spack package:
- Versions:
- 1.12.1
- Build Dependencies:
- libpng, hdf, hdf5, libmatheval, octave
- Link Dependencies:
- libpng, hdf, hdf5, libmatheval, octave
- Description:
- h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format.
h5z-zfp¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.7.0
- Build Dependencies:
- hdf5, zfp
- Link Dependencies:
- hdf5, zfp
- Description:
- A highly flexible floating point and integer compression plugin for the HDF5 library using ZFP compression.
hacckernels¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake
- Description:
- HACCKernels: A Benchmark for HACC's Particle Force Kernels. The Hardware/Hybrid Accelerated Cosmology Code (HACC), a cosmology N-body- code framework, is designed to run efficiently on diverse computing architectures and to scale to millions of cores and beyond.
hadoop¶
- Homepage:
- Spack package:
- Versions:
- 2.9.0
- Run Dependencies:
- java
- Description:
- The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
hapcut2¶
- Homepage:
- Spack package:
- Versions:
- 2017-07-10
- Description:
- HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to 'just work' with excellent speed and accuracy.
haploview¶
- Homepage:
- Spack package:
- Versions:
- 4.1
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- Haploview is designed to simplify and expedite the process of haplotype analysis.
harfbuzz¶
- Homepage:
- Spack package:
- Versions:
- 1.4.6, 0.9.37
- Build Dependencies:
- zlib, cairo, icu4c, pkgconfig, freetype, glib
- Link Dependencies:
- zlib, freetype, cairo, icu4c, glib
- Description:
- The Harfbuzz package contains an OpenType text shaping engine.
harminv¶
- Homepage:
- Spack package:
- Versions:
- 1.4
- Build Dependencies:
- lapack, blas
- Link Dependencies:
- lapack, blas
- Description:
- Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
hdf¶
- Homepage:
- Spack package:
- Versions:
- 4.2.13, 4.2.12, 4.2.11
- Build Dependencies:
- zlib, bison, jpeg, szip, flex
- Link Dependencies:
- zlib, jpeg, szip
- Description:
- HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.
hdf5¶
- Homepage:
- Spack package:
- Versions:
- 1.10.1, 1.10.0-patch1, 1.10.0, 1.8.19, 1.8.18, 1.8.17, 1.8.16, 1.8.15, 1.8.14, 1.8.13, 1.8.12
- Build Dependencies:
- numactl, zlib, szip, mpi
- Link Dependencies:
- numactl, zlib, szip, mpi
- Description:
- HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
hdf5-blosc¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- hdf5, libtool, c-blosc
- Link Dependencies:
- hdf5, c-blosc
- Description:
- Blosc filter for HDF5
help2man¶
- Homepage:
- Spack package:
- Versions:
- 1.47.4
- Build Dependencies:
- gettext
- Description:
- help2man produces simple manual pages from the '--help' and '--version' output of other commands.
hepmc¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.06.09, 2.06.08, 2.06.07, 2.06.06, 2.06.05
- Build Dependencies:
- cmake
- Description:
- The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.
heppdt¶
- Homepage:
- Spack package:
- Versions:
- 3.04.01, 3.04.00, 3.03.02, 3.03.01, 3.03.00, 2.06.01
- Description:
- The HepPID library contains translation methods for particle ID's to and from various Monte Carlo generators and the PDG standard numbering scheme. We realize that the generators adhere closely to the standard, but there are occasional differences.
highfive¶
- Homepage:
- Spack package:
- Versions:
- 1.5, 1.2, 1.1, 1.0
- Build Dependencies:
- hdf5, cmake, boost
- Link Dependencies:
- hdf5, boost
- Description:
- HighFive - Header only C++ HDF5 interface
highwayhash¶
- Homepage:
- Spack package:
- Versions:
- dfcb97
- Description:
- Strong (well-distributed and unpredictable) hashes: - Portable implementation of SipHash - HighwayHash, a 5x faster SIMD hash with security claims
hisat2¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Description:
- HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).
hmmer¶
- Homepage:
- Spack package:
- Versions:
- 3.1b2, 3.0, 2.4i, 2.3.2, 2.3.1
- Build Dependencies:
- gsl, mpi
- Link Dependencies:
- gsl, mpi
- Description:
- HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
hoomd-blue¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1.6
- Build Dependencies:
- py-numpy, cuda, doxygen, mpi, pkgconfig, python, cmake
- Link Dependencies:
- cuda, python, mpi
- Run Dependencies:
- py-numpy
- Description:
- HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.
hpccg¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. Intended to be the 'best approximation to an unstructured implicit finite element or finite volume application in 800 lines or fewer.'
hpctoolkit¶
- Homepage:
- Spack package:
- Versions:
- 2017.06, master
- Build Dependencies:
- papi, hpctoolkit-externals, mpi
- Link Dependencies:
- papi, hpctoolkit-externals, mpi
- Description:
- HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.
hpctoolkit-externals¶
- Homepage:
- Spack package:
- Versions:
- 2017.06, master
- Description:
- HPCToolkit performance analysis tool has many prerequisites and HpctoolkitExternals package provides all these prerequisites.
hpgmg¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cuda, petsc, python, mpi
- Link Dependencies:
- cuda, petsc, mpi
- Description:
- HPGMG implements full multigrid (FMG) algorithms using finite-volume and finite-element methods. Different algorithmic variants adjust the arithmetic intensity and architectural properties that are tested. These FMG methods converge up to discretization error in one F-cycle, thus may be considered direct solvers. An F-cycle visits the finest level a total of two times, the first coarsening (8x smaller) 4 times, the second coarsening 6 times, etc.
hpl¶
- Homepage:
- Spack package:
- Versions:
- 2.2
- Build Dependencies:
- mpi, blas
- Link Dependencies:
- mpi, blas
- Description:
- HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.
hpx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- cmake, hwloc, boost
- Link Dependencies:
- hwloc, boost
- Description:
- C++ runtime system for parallel and distributed applications.
hpx5¶
- Homepage:
- Spack package:
- Versions:
- 4.1.0, 4.0.0, 3.1.0, 2.0.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0
- Build Dependencies:
- opencl, autoconf, m4, libtool, mpi, pkgconfig, automake, hwloc, metis, jemalloc
- Link Dependencies:
- opencl, metis, hwloc, jemalloc, mpi
- Description:
- The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an open source, portable, performance-oriented runtime developed at CREST (Indiana University). HPX-5 provides a distributed programming model allowing programs to run unmodified on systems from a single SMP to large clusters and supercomputers with thousands of nodes. HPX-5 supports a wide variety of Intel and ARM platforms. It is being used by a broad range of scientific applications enabling scientists to write code that performs and scales better than contemporary runtimes.
hsakmt¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Description:
- hsakmt is a thunk library that provides a userspace interface to amdkfd (AMD's HSA Linux kernel driver). It is the HSA equivalent of libdrm.
hstr¶
- Homepage:
- Spack package:
- Versions:
- 1.22
- Build Dependencies:
- autoconf, m4, libtool, automake, ncurses, readline
- Link Dependencies:
- ncurses, readline
- Description:
- hstr(hh) is a shell history suggest box for Bash and Zsh, which enables easy viewing, searching and using your command history.
htop¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- htop is an interactive text-mode process viewer for Unix systems.
htslib¶
- Homepage:
- Spack package:
- Versions:
- 1.6, 1.4, 1.3.1, 1.2
- Build Dependencies:
- autoconf, m4, zlib, libtool, bzip2, automake, xz
- Link Dependencies:
- autoconf, m4, zlib, libtool, bzip2, automake, xz
- Description:
- C library for high-throughput sequencing data formats.
httpie¶
- Homepage:
- Spack package:
- Versions:
- 0.9.9, 0.9.8
- Build Dependencies:
- py-requests, py-pysocks, python, py-setuptools, py-argparse, py-pygments
- Link Dependencies:
- python
- Run Dependencies:
- py-requests, py-pysocks, python, py-setuptools, py-argparse, py-pygments
- Description:
- Modern command line HTTP client.
hub¶
- Homepage:
- Spack package:
- Versions:
- 2.2.3, 2.2.2, 2.2.1, 2.2.0, 1.12.4, head
- Build Dependencies:
- go
- Link Dependencies:
- go
- Description:
- The github git wrapper
hunspell¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- The most popular spellchecking library (sez the author...).
hwloc¶
- Homepage:
- Spack package:
- Versions:
- 1.11.8, 1.11.7, 1.11.6, 1.11.5, 1.11.4, 1.11.3, 1.11.2, 1.11.1, 1.9
- Build Dependencies:
- cuda, pkgconfig, libpciaccess, libxml2
- Link Dependencies:
- cuda, libpciaccess, libxml2
- Description:
- The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
hybpiper¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- py-biopython, bwa, blast-plus, parallel, spades, exonerate, python, samtools
- Link Dependencies:
- samtools, bwa, exonerate, parallel, blast-plus, spades
- Run Dependencies:
- python, py-biopython
- Description:
- HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads
hydra¶
- Homepage:
- Spack package:
- Versions:
- 3.2
- Description:
- Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource management systems (such as slurm, pbs, sge).
hypre¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.13.0, 2.12.1, 2.11.2, 2.11.1, 2.10.1, 2.10.0b, xsdk-0.2.0
- Build Dependencies:
- lapack, mpi, blas
- Link Dependencies:
- lapack, mpi, blas
- Description:
- Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.
i3¶
- Homepage:
- Spack package:
- Versions:
- 4.14.1
- Build Dependencies:
- xcb-util-xrm, xcb-util-keysyms, libxkbcommon, xcb-util-wm, libtool, startup-notification, libev, xcb-util-cursor, m4, autoconf, pkg-config, cairo, pango, automake, yajl
- Link Dependencies:
- xcb-util-xrm, xcb-util-keysyms, libxkbcommon, xcb-util-wm, cairo, pango, startup-notification, libev, xcb-util-cursor, yajl
- Description:
- i3, improved tiling wm. i3 is a tiling window manager, completely written from scratch. The target platforms are GNU/Linux and BSD operating systems, our code is Free and Open Source Software (FOSS) under the BSD license. i3 is primarily targeted at advanced users and developers.
ibmisc¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0
- Build Dependencies:
- py-numpy, udunits2, everytrace, cmake, blitz, doxygen, py-cython, proj, eigen, netcdf-cxx4, python, googletest, boost
- Link Dependencies:
- everytrace, proj, eigen, netcdf-cxx4, python, udunits2, blitz, boost
- Run Dependencies:
- py-numpy, py-cython
- Description:
- Misc. reusable utilities used by IceBin.
iceauth¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- pkgconfig, xproto, libice, util-macros
- Link Dependencies:
- libice
- Description:
- The iceauth program is used to edit and display the authorization information used in connecting with ICE. It operates very much like the xauth program for X11 connection authentication records.
icedtea¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0
- Build Dependencies:
- libpng, libxi, zlib, libxt, alsa-lib, jpeg, libxext, libxrender, freetype, cups, libxau, libxinerama, libxcomposite, lcms, xproto, pkgconfig, wget, gmake, gtkplus, libx11, giflib, libxdmcp, jdk, libxtst
- Link Dependencies:
- libpng, libxi, zlib, libxdmcp, lcms, libxt, alsa-lib, jpeg, libxcomposite, libxext, gtkplus, libxrender, freetype, libx11, giflib, cups, libxau, libxinerama, libxtst, xproto
- Description:
- The IcedTea project provides a harness to build the source code from http://openjdk.java.net using Free Software build tools and adds a number of key features to the upstream OpenJDK codebase. IcedTea requires an existing IcedTea or OpenJDK install to build.
icet¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- The Image Composition Engine for Tiles (IceT) is a high-performance sort-last parallel rendering library.
ico¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- ico is a simple animation program that may be used for testing various X11 operations and extensions. It displays a wire-frame rotating polyhedron, with hidden lines removed, or a solid-fill polyhedron with hidden faces removed.
icu4c¶
- Homepage:
- Spack package:
- Versions:
- 60.1, 58.2, 57.1
- Description:
- ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.
id3lib¶
- Homepage:
- Spack package:
- Versions:
- 3.8.3
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Library for manipulating ID3v1 and ID3v2 tags
idba¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
igraph¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1
- Build Dependencies:
- libxml2
- Link Dependencies:
- libxml2
- Description:
- igraph is a library for creating and manipulating graphs.
igv¶
- Homepage:
- Spack package:
- Versions:
- 2.4.5, 2.3.50
- Build Dependencies:
- ant, jdk
- Run Dependencies:
- jdk
- Description:
- The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
ilmbase¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.0, 2.0.1, 1.0.2, 0.9.0
- Description:
- OpenEXR ILM Base libraries (high dynamic-range image file format)
image-magick¶
- Homepage:
- Spack package:
- Versions:
- 7.0.5-9, 7.0.2-7, 7.0.2-6
- Build Dependencies:
- libpng, fontconfig, freetype, libtool, pango, ghostscript, libtiff, jpeg, ghostscript-fonts
- Link Dependencies:
- libpng, fontconfig, freetype, ghostscript-fonts, pango, ghostscript, libtiff, jpeg
- Description:
- ImageMagick is a software suite to create, edit, compose, or convert bitmap images.
imake¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- pkgconfig, xproto
- Description:
- The imake build system.
impute2¶
- Homepage:
- Spack package:
- Versions:
- 2.3.2
- Description:
- IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009.
infernal¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).
inputproto¶
- Homepage:
- Spack package:
- Versions:
- 2.3.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Input Extension. This extension defines a protocol to provide additional input devices management such as graphic tablets.
intel¶
- Homepage:
- Spack package:
- Versions:
- 18.0.1, 18.0.0, 17.0.4, 17.0.3, 17.0.2, 17.0.1, 17.0.0, 16.0.4, 16.0.3, 16.0.2
- Description:
- Intel Compilers.
intel-daal¶
- Homepage:
- Spack package:
- Versions:
- 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 2016.3.210, 2016.2.181
- Description:
- Intel Data Analytics Acceleration Library.
intel-gpu-tools¶
- Homepage:
- Spack package:
- Versions:
- 1.16
- Build Dependencies:
- libdrm, libpciaccess, cairo, util-macros, flex, pkgconfig, bison, python, glib
- Link Dependencies:
- libdrm, libpciaccess, cairo, glib
- Description:
- Intel GPU Tools is a collection of tools for development and testing of the Intel DRM driver. There are many macro-level test suites that get used against the driver, including xtest, rendercheck, piglit, and oglconform, but failures from those can be difficult to track down to kernel changes, and many require complicated build procedures or specific testing environments to get useful results. Therefore, Intel GPU Tools includes low-level tools and tests specifically for development and testing of the Intel DRM Driver.
intel-ipp¶
- Homepage:
- Spack package:
- Versions:
- 2018.1.163, 2018.0.128, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 9.0.3.210
- Description:
- Intel Integrated Performance Primitives.
intel-mkl¶
- Homepage:
- Spack package:
- Versions:
- 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 11.3.3.210, 11.3.2.181
- Description:
- Intel Math Kernel Library.
intel-mkl-dnn¶
- Homepage:
- Spack package:
- Versions:
- 0.11, 0.10, 0.9
- Build Dependencies:
- intel-mkl, cmake
- Link Dependencies:
- intel-mkl
- Description:
- Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL- DNN).
intel-mpi¶
- Homepage:
- Spack package:
- Versions:
- 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 5.1.3.223
- Description:
- Intel MPI
intel-parallel-studio¶
- Homepage:
- Spack package:
- Versions:
- professional.2018.1, professional.2018.0, professional.2017.4, professional.2017.3, professional.2017.2, professional.2017.1, professional.2017.0, professional.2016.4, professional.2016.3, professional.2016.2, professional.2015.6, composer.2018.1, composer.2018.0, composer.2017.4, composer.2017.3, composer.2017.2, composer.2017.1, composer.2017.0, composer.2016.4, composer.2016.3, composer.2016.2, composer.2015.6, cluster.2018.1, cluster.2018.0, cluster.2017.5, cluster.2017.4, cluster.2017.3, cluster.2017.2, cluster.2017.1, cluster.2017.0, cluster.2016.4, cluster.2016.3, cluster.2016.2, cluster.2015.6
- Description:
- Intel Parallel Studio.
intel-tbb¶
- Homepage:
- Spack package:
- Versions:
- 2018.2, 2018.1, 2018.0, 2017.8, 2017.6, 2017.5, 2017.3, 4.4.4, 4.4.3
- Description:
- Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.
intltool¶
- Homepage:
- Spack package:
- Versions:
- 0.51.0
- Build Dependencies:
- perl, perl-xml-parser
- Run Dependencies:
- perl, perl-xml-parser
- Description:
- intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
ior¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1
- Build Dependencies:
- autoconf, m4, libtool, mpi, automake, parallel-netcdf, hdf5
- Link Dependencies:
- parallel-netcdf, hdf5, mpi
- Description:
- The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.
iozone¶
- Homepage:
- Spack package:
- Versions:
- 3_465
- Description:
- IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.
ipopt¶
- Homepage:
- Spack package:
- Versions:
- 3.12.9, 3.12.8, 3.12.7, 3.12.6, 3.12.5, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0
- Build Dependencies:
- coinhsl, metis, mumps, pkgconfig, lapack, blas
- Link Dependencies:
- coinhsl, lapack, metis, mumps, blas
- Description:
- Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.
isaac¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.3.3, 1.3.2, 1.3.1, 1.3.0, master
- Build Dependencies:
- cmake
- Link Dependencies:
- cuda, icet, boost, jansson, mpi, jpeg
- Description:
- In Situ Animation of Accelerated Computations: Header-Only Library
isaac-server¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.3.2, 1.3.1, 1.3.0, master
- Build Dependencies:
- cmake
- Link Dependencies:
- libwebsockets, jpeg, jansson, boost
- Description:
- In Situ Animation of Accelerated Computations: Server
isl¶
- Homepage:
- Spack package:
- Versions:
- 0.18, 0.14
- Build Dependencies:
- gmp
- Link Dependencies:
- gmp
- Description:
- isl (Integer Set Library) is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints.
itstool¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2, 2.0.1, 2.0.0, 1.2.0
- Description:
- ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.
itsx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.11
- Build Dependencies:
- perl, hmmer
- Link Dependencies:
- hmmer
- Run Dependencies:
- perl
- Description:
- Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
jags¶
- Homepage:
- Spack package:
- Versions:
- 4.2.0
- Build Dependencies:
- lapack, blas
- Link Dependencies:
- lapack, blas
- Description:
- JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS
jansson¶
- Homepage:
- Spack package:
- Versions:
- 2.9
- Build Dependencies:
- cmake
- Description:
- Jansson is a C library for encoding, decoding and manipulating JSON data.
jasper¶
- Homepage:
- Spack package:
- Versions:
- 1.900.1
- Build Dependencies:
- jpeg
- Link Dependencies:
- jpeg
- Description:
- Library for manipulating JPEG-2000 images
jbigkit¶
- Homepage:
- Spack package:
- Versions:
- 2.1, 1.6
- Description:
- JBIG-Kit is a software implementation of the JBIG1 data compression standard.
jdk¶
- Homepage:
- Spack package:
- Versions:
- 8u141-b15, 8u131-b11, 8u92-b14, 8u73-b02, 8u66-b17, 7u80-b0
- Description:
- The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers.
jellyfish¶
- Homepage:
- Spack package:
- Versions:
- 2.2.7, 1.1.11
- Build Dependencies:
- perl, python
- Run Dependencies:
- perl, python
- Description:
- JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.
jemalloc¶
- Homepage:
- Spack package:
- Versions:
- 4.5.0, 4.4.0, 4.3.1, 4.2.1, 4.2.0, 4.1.0, 4.0.4
- Description:
- jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
jmol¶
- Homepage:
- Spack package:
- Versions:
- 14.8.0
- Run Dependencies:
- java
- Description:
- Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.
jq¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- bison, oniguruma
- Link Dependencies:
- oniguruma
- Description:
- jq is a lightweight and flexible command-line JSON processor.
json-c¶
- Homepage:
- Spack package:
- Versions:
- 0.12.1, 0.11
- Build Dependencies:
- autoconf
- Description:
- A JSON implementation in C.
json-cwx¶
- Homepage:
- Spack package:
- Versions:
- 0.12
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- JSON-C with Extensions
json-glib¶
- Homepage:
- Spack package:
- Versions:
- 1.2.8
- Build Dependencies:
- glib
- Link Dependencies:
- glib
- Description:
- JSON-GLib is a library for reading and parsing JSON using GLib and GObject data types and API.
jsoncpp¶
- Homepage:
- Spack package:
- Versions:
- 1.7.3
- Build Dependencies:
- cmake
- Description:
- JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
judy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Description:
- Judy: General-purpose dynamic array, associative array and hash-trie.
julia¶
- Homepage:
- Spack package:
- Versions:
- 0.5.2, 0.5.1, 0.5.0, 0.4.7, 0.4.6, 0.4.5, 0.4.3, release-0.5, release-0.4, master
- Build Dependencies:
- m4, openssl, curl, cmake, binutils, python, git
- Link Dependencies:
- binutils, openssl, cmake, curl, python, git
- Run Dependencies:
- py-matplotlib, hdf5, mpi
- Description:
- The Julia Language: A fresh approach to technical computing
kahip¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.00
- Build Dependencies:
- scons, mpi, argtable
- Link Dependencies:
- mpi, argtable
- Description:
- KaHIP - Karlsruhe High Quality Partitioning - is a family of graph partitioning programs. It includes KaFFPa (Karlsruhe Fast Flow Partitioner), which is a multilevel graph partitioning algorithm, in its variants Strong, Eco and Fast, KaFFPaE (KaFFPaEvolutionary) which is a parallel evolutionary algorithm that uses KaFFPa to provide combine and mutation operations, as well as KaBaPE which extends the evolutionary algorithm. Moreover, specialized techniques are included to partition road networks (Buffoon), to output a vertex separator from a given partition or techniques geared towards efficient partitioning of social networks.
kaks-calculator¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Description:
- KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.
kaldi¶
- Homepage:
- Spack package:
- Versions:
- master, c024e8
- Build Dependencies:
- cuda, openfst, blas
- Link Dependencies:
- cuda, openfst, blas
- Run Dependencies:
- sph2pipe, speex, sctk
- Description:
- Kaldi is a toolkit for speech recognition written in C++ and licensed under the Apache License v2.0. Kaldi is intended for use by speech recognition researchers.
kallisto¶
- Homepage:
- Spack package:
- Versions:
- 0.43.1
- Build Dependencies:
- cmake, hdf5, zlib, mpich
- Link Dependencies:
- mpich, hdf5, zlib
- Description:
- kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.
kbproto¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Keyboard Extension. This extension defines a protcol to provide a number of new capabilities and controls for text keyboards.
kdiff3¶
- Homepage:
- Spack package:
- Versions:
- 0.9.98
- Build Dependencies:
- qt
- Link Dependencies:
- qt
- Description:
- Compare and merge 2 or 3 files or directories.
kealib¶
- Homepage:
- Spack package:
- Versions:
- 1.4.5
- Build Dependencies:
- hdf5, cmake
- Link Dependencies:
- hdf5
- Description:
- An HDF5 Based Raster File Format KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. Development work on this project has been funded by Landcare Research.
kentutils¶
- Homepage:
- Spack package:
- Versions:
- 302.1
- Build Dependencies:
- libpng, mariadb, openssl
- Link Dependencies:
- libpng, mariadb, openssl
- Description:
- Jim Kent command line bioinformatic utilities
kmergenie¶
- Homepage:
- Spack package:
- Versions:
- 1.7044
- Build Dependencies:
- python, py-setuptools, zlib, r
- Link Dependencies:
- zlib
- Run Dependencies:
- python, py-setuptools, r
- Description:
- KmerGenie estimates the best k-mer length for genome de novo assembly.
kokkos¶
- Homepage:
- Spack package:
- Versions:
- 2.03.00
- Build Dependencies:
- cuda, hwloc, qthreads
- Link Dependencies:
- cuda, hwloc, qthreads
- Description:
- Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms.
kraken¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- perl, jellyfish
- Link Dependencies:
- jellyfish
- Run Dependencies:
- perl
- Description:
- Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
krims¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.2.1
- Build Dependencies:
- cmake
- Description:
- The bucket of Krimskrams every C or C++ project needs
kripke¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- Kripke is a simple, scalable, 3D Sn deterministic particle transport proxy/mini app.
laghos¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- mpi, mfem
- Link Dependencies:
- mpi, mfem
- Description:
- Laghos (LAGrangian High-Order Solver) is a CEED miniapp that solves the time-dependent Euler equations of compressible gas dynamics in a moving Lagrangian frame using unstructured high-order finite element spatial discretization and explicit high-order time-stepping.
lammps¶
- Homepage:
- Spack package:
- Versions:
- develop, 20170922, 20170901
- Build Dependencies:
- netcdf, fftw, voropp, mpi, lapack, cmake, latte, python, hdf5, blas
- Link Dependencies:
- netcdf, fftw, voropp, mpi, lapack, latte, python, hdf5, blas
- Description:
- LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion.
last¶
- Homepage:
- Spack package:
- Versions:
- 869
- Description:
- LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads).
latte¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0.1
- Build Dependencies:
- lapack, cmake, blas, qmd-progress, mpi
- Link Dependencies:
- lapack, blas, qmd-progress, mpi
- Description:
- Open source density functional tight binding molecular dynamics.
launchmon¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- spectrum-mpi, libgcrypt, boost, automake, libgpg-error, autoconf, libtool
- Link Dependencies:
- spectrum-mpi, libgcrypt, boost, elf, libgpg-error
- Description:
- Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.
lazyten¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.4.1
- Build Dependencies:
- arpack-ng, lapack, krims, armadillo, cmake, blas
- Link Dependencies:
- lapack, arpack-ng, armadillo, blas, krims
- Description:
- Lightweight linear algebra library based on lazy matrices
lbann¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.93, 0.92, 0.91
- Build Dependencies:
- cuda, opencv, cub, mpi, cudnn, nccl, protobuf, cmake, elemental, hwloc, cnpy
- Link Dependencies:
- cuda, opencv, cub, mpi, hwloc, nccl, protobuf, cudnn, elemental, cnpy
- Description:
- LBANN: Livermore Big Artificial Neural Network Toolkit. A distributed memory, HPC-optimized, model and data parallel training toolkit for deep neural networks.
lbxproxy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libxext, liblbxutil, libx11, util-macros, pkgconfig, xproxymanagementprotocol, xtrans, libice, bigreqsproto
- Link Dependencies:
- libxext, liblbxutil, libx11, libice
- Description:
- lbxproxy accepts client connections, multiplexes them over a single connection to the X server, and performs various optimizations on the X protocol to make it faster over low bandwidth and/or high latency connections. Note that the X server source from X.Org no longer supports the LBX extension, so this program is only useful in connecting to older X servers.
lcals¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Description:
- LCALS ("Livermore Compiler Analysis Loop Suite") is a collection of loop kernels based, in part, on historical "Livermore Loops" benchmarks (See the 1986 technical report: "The Livermore Fortran Kernels: A Computer Test of the Numerical Performance Range", by Frank H. McMahon, UCRL-53745.). The suite contains facilities to generate timing statistics and reports.
lcms¶
- Homepage:
- Spack package:
- Versions:
- 2.8, 2.6
- Build Dependencies:
- libtiff, zlib, jpeg
- Link Dependencies:
- libtiff, zlib, jpeg
- Description:
- Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license).
ldc¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- llvm, zlib, libconfig, curl, ldc-bootstrap, libedit, binutils, cmake
- Link Dependencies:
- llvm, zlib, libconfig, curl, ldc-bootstrap, libedit, binutils
- Run Dependencies:
- binutils
- Description:
- The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC
ldc-bootstrap¶
- Homepage:
- Spack package:
- Versions:
- 0.17.4
- Build Dependencies:
- llvm, zlib, libconfig, curl, libedit, binutils, cmake
- Link Dependencies:
- llvm, zlib, libconfig, curl, libedit, binutils
- Description:
- The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC This old version of the compiler is needed to bootstrap newer ones.
legion¶
- Homepage:
- Spack package:
- Versions:
- develop, 17.10.0, 17.08.0, 17.02.0
- Build Dependencies:
- cmake, gasnet
- Link Dependencies:
- gasnet
- Description:
- Legion is a data-centric parallel programming system for writing portable high performance programs targeted at distributed heterogeneous architectures. Legion presents abstractions which allow programmers to describe properties of program data (e.g. independence, locality). By making the Legion programming system aware of the structure of program data, it can automate many of the tedious tasks programmers currently face, including correctly extracting task- and data-level parallelism and moving data around complex memory hierarchies. A novel mapping interface provides explicit programmer controlled placement of data in the memory hierarchy and assignment of tasks to processors in a way that is orthogonal to correctness, thereby enabling easy porting and tuning of Legion applications to new architectures.
leveldb¶
- Homepage:
- Spack package:
- Versions:
- 1.20, 1.18
- Build Dependencies:
- snappy
- Link Dependencies:
- snappy
- Description:
- LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
lftp¶
- Homepage:
- Spack package:
- Versions:
- 4.8.1, 4.7.7, 4.6.4
- Build Dependencies:
- ncurses, openssl, libiconv, expat, zlib, readline
- Link Dependencies:
- ncurses, openssl, libiconv, expat, zlib, readline
- Description:
- LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
libaec¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2, 1.0.1, 1.0.0
- Build Dependencies:
- cmake
- Description:
- Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library.
libaio¶
- Homepage:
- Spack package:
- Versions:
- 0.3.110
- Description:
- This is the linux native Asynchronous I/O interface library.
libapplewm¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- libxext, libx11, util-macros, pkgconfig, applewmproto, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- AppleWM is a simple library designed to interface with the Apple-WM extension. This extension allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.
libarchive¶
- Homepage:
- Spack package:
- Versions:
- 3.3.2, 3.2.1, 3.1.2, 3.1.1, 3.1.0
- Build Dependencies:
- openssl, lz4, zlib, xz, bzip2, expat, nettle, lzo, libxml2, lzma
- Link Dependencies:
- openssl, lz4, zlib, xz, bzip2, expat, nettle, lzo, libxml2, lzma
- Description:
- libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats.
libassuan¶
- Homepage:
- Spack package:
- Versions:
- 2.4.5, 2.4.3
- Build Dependencies:
- libgpg-error
- Link Dependencies:
- libgpg-error
- Description:
- Libassuan is a small library implementing the so-called Assuan protocol.
libatomic-ops¶
- Homepage:
- Spack package:
- Versions:
- 7.4.4
- Description:
- This package provides semi-portable access to hardware-provided atomic memory update operations on a number architectures.
libbeagle¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2
- Build Dependencies:
- autoconf, m4, libtool, pkgconfig, automake, subversion
- Description:
- Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
libbsd¶
- Homepage:
- Spack package:
- Versions:
- 0.8.6
- Description:
- This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project.
libbson¶
- Homepage:
- Spack package:
- Versions:
- 1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- libbson is a library providing useful routines related to building, parsing, and iterating BSON documents.
libcanberra¶
- Homepage:
- Spack package:
- Versions:
- 0.30
- Build Dependencies:
- libxcomposite, libxrandr, libxdamage, libxfixes, libxcursor, libxcb, libxext, gtkplus, libxrender, libx11, libvorbis, libxau, libxinerama, pkgconfig
- Link Dependencies:
- libxcomposite, libxrandr, libxdamage, libxfixes, libxcursor, libxext, gtkplus, libxrender, libx11, libvorbis, libxau, libxinerama, libxcb
- Description:
- libcanberra is an implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME.
libcap¶
- Homepage:
- Spack package:
- Versions:
- 2.25
- Description:
- Libcap implements the user-space interfaces to the POSIX 1003.1e capabilities available in Linux kernels. These capabilities are a partitioning of the all powerful root privilege into a set of distinct privileges.
libcerf¶
- Homepage:
- Spack package:
- Versions:
- 1.3
- Description:
- A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian
libcint¶
- Homepage:
- Spack package:
- Versions:
- 3.0.4
- Build Dependencies:
- py-numpy, cmake, python, blas
- Link Dependencies:
- blas
- Test Dependencies:
- py-numpy, python
- Description:
- Library for analytical Gaussian integrals for quantum chemistry.
libcircle¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1-rc.1
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.
libconfig¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- C/C++ Configuration File Library
libcroco¶
- Homepage:
- Spack package:
- Versions:
- 0.6.12
- Build Dependencies:
- glib, libxml2
- Link Dependencies:
- glib, libxml2
- Description:
- Libcroco is a standalone css2 parsing and manipulation library.
libctl¶
- Homepage:
- Spack package:
- Versions:
- 3.2.2
- Build Dependencies:
- guile
- Link Dependencies:
- guile
- Description:
- libctl is a free Guile-based library implementing flexible control files for scientific simulations.
libdivsufsort¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- cmake
- Description:
- libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.
libdmx¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- libxext, libx11, util-macros, pkgconfig, dmxproto, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- libdmx - X Window System DMX (Distributed Multihead X) extension library.
libdrm¶
- Homepage:
- Spack package:
- Versions:
- 2.4.81, 2.4.75, 2.4.70, 2.4.59, 2.4.33
- Build Dependencies:
- pkgconfig, libpthread-stubs, libpciaccess
- Link Dependencies:
- libpthread-stubs, libpciaccess
- Description:
- A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface.
libdwarf¶
- Homepage:
- Spack package:
- Versions:
- 20160507, 20130729, 20130207, 20130126
- Link Dependencies:
- zlib, elf
- Description:
- The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and any one interested in reading or writing DWARF information). It was developed by a committee (known as the PLSIG at the time) starting around 1991. Starting around 1991 SGI developed the libdwarf and dwarfdump tools for internal use and as part of SGI IRIX developer tools. Since that time dwarfdump and libdwarf have been shipped (as an executable and archive respectively, not source) with every release of the SGI MIPS/IRIX C compiler.
libedit¶
- Homepage:
- Spack package:
- Versions:
- 3.1-20170329, 3.1-20160903, 3.1-20150325
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- An autotools compatible port of the NetBSD editline library
libelf¶
- Homepage:
- Spack package:
- Versions:
- 0.8.13, 0.8.12
- Description:
- libelf lets you read, modify or create ELF object files in an architecture-independent way. The library takes care of size and endian issues, e.g. you can process a file for SPARC processors on an Intel- based system.
libemos¶
- Homepage:
- Spack package:
- Versions:
- 4.5.1, 4.5.0, 4.4.9, 4.4.7, 4.4.2
- Build Dependencies:
- pkgconfig, grib-api, eccodes, fftw, cmake
- Link Dependencies:
- grib-api, eccodes, fftw
- Description:
- The Interpolation library (EMOSLIB) includes Interpolation software and BUFR & CREX encoding/decoding routines.
libepoxy¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Description:
- Epoxy is a library for handling OpenGL function pointer management for you.
libev¶
- Homepage:
- Spack package:
- Versions:
- develop, 4.24
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- A full-featured and high-performance event loop that is loosely modelled after libevent, but without its limitations and bugs.
libevent¶
- Homepage:
- Spack package:
- Versions:
- 2.0.21, 2.0.20, 2.0.19, 2.0.18, 2.0.17, 2.0.16, 2.0.15, 2.0.14, 2.0.13, 2.0.12
- Build Dependencies:
- openssl
- Link Dependencies:
- openssl
- Description:
- The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
libevpath¶
- Homepage:
- Spack package:
- Versions:
- develop, 4.2.1, 4.1.2, 4.1.1
- Build Dependencies:
- libffs, cmake
- Link Dependencies:
- libffs
- Description:
- EVpath is an event transport middleware layer designed to allow for the easy implementation of overlay networks, with active data processing, routing and management at all points in the overlay. EVPath is designed for high performance systems.
libfabric¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0, 1.4.2
- Description:
- The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications.
libffi¶
- Homepage:
- Spack package:
- Versions:
- 3.2.1
- Description:
- The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time.
libffs¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1.1, 1.1
- Build Dependencies:
- gtkorvo-atl, gtkorvo-dill, flex, cmake, bison, gtkorvo-cercs-env
- Link Dependencies:
- gtkorvo-cercs-env, gtkorvo-atl, bison, gtkorvo-dill, flex
- Description:
- FFS is a middleware library for data communication, including representation, processing and marshaling that preserves the performance of traditional approaches while relaxing the requirement of a priori knowledge and providing complex run-time flexibility.
libfontenc¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- pkgconfig, xproto, zlib, util-macros
- Link Dependencies:
- zlib
- Description:
- libfontenc - font encoding library.
libfs¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- pkgconfig, xproto, xtrans, util-macros, fontsproto
- Description:
- libFS - X Font Service client library. This library is used by clients of X Font Servers (xfs), such as xfsinfo, fslsfonts, and the X servers themselves.
libgcrypt¶
- Homepage:
- Spack package:
- Versions:
- 1.8.1, 1.7.6, 1.6.2
- Build Dependencies:
- libgpg-error
- Link Dependencies:
- libgpg-error
- Description:
- Libgcrypt is a general purpose cryptographic library based on the code from GnuPG. It provides functions for all cryptographic building blocks: symmetric ciphers, hash algorithms, MACs, public key algorithms, large integer functions, random numbers and a lot of supporting functions.
libgd¶
- Homepage:
- Spack package:
- Versions:
- 2.2.4, 2.2.3, 2.1.1
- Build Dependencies:
- libpng, fontconfig, autoconf, m4, libtool, gettext, libiconv, pkgconfig, automake, libtiff, jpeg
- Link Dependencies:
- libpng, fontconfig, libtiff, jpeg, libiconv
- Description:
- GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and "wrappers" are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development.
libgit2¶
- Homepage:
- Spack package:
- Versions:
- 0.26.0, 0.24.2
- Build Dependencies:
- cmake, libssh2
- Link Dependencies:
- libssh2
- Description:
- libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.
libgpg-error¶
- Homepage:
- Spack package:
- Versions:
- 1.27, 1.21, 1.18
- Description:
- Libgpg-error is a small library that defines common error values for all GnuPG components. Among these are GPG, GPGSM, GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry, SmartCard Daemon and possibly more in the future.
libgpuarray¶
- Homepage:
- Spack package:
- Versions:
- 0.6.2, 0.6.1, 0.6.0
- Build Dependencies:
- cuda, cmake, python
- Link Dependencies:
- cuda, python
- Description:
- Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test.
libgridxc¶
- Homepage:
- Spack package:
- Versions:
- 0.7.6
- Description:
- A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems.
libharu¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0, 2.2.0, master
- Build Dependencies:
- libpng, automake, autoconf, zlib, libtool
- Link Dependencies:
- libpng, zlib
- Description:
- libharu - free PDF library. Haru is a free, cross platform, open-sourced software library for generating PDF.
libhio¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0.0, 1.3.0.1
- Build Dependencies:
- pkgconfig, json-c, bzip2
- Link Dependencies:
- json-c, bzip2
- Description:
- A library for writing to hierarchical data store systems.
libice¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- pkgconfig, xproto, xtrans, util-macros
- Description:
- libICE - Inter-Client Exchange Library.
libiconv¶
- Homepage:
- Spack package:
- Versions:
- 1.15, 1.14
- Description:
- GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.
libint¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.0, 1.1.6, 1.1.5
- Build Dependencies:
- automake, autoconf, libtool, boost, gmp
- Link Dependencies:
- boost, gmp
- Description:
- Libint is a high-performance library for computing Gaussian integrals in quantum mechanics.
libjpeg¶
- Homepage:
- Spack package:
- Versions:
- 9b, 9a
- Description:
- libjpeg is a widely used free library with functions for handling the JPEG image data format. It implements a JPEG codec (encoding and decoding) alongside various utilities for handling JPEG data.
libjpeg-turbo¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0, 1.3.1
- Build Dependencies:
- nasm
- Description:
- libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libksba¶
- Homepage:
- Spack package:
- Versions:
- 1.3.5
- Build Dependencies:
- libgpg-error
- Link Dependencies:
- libgpg-error
- Description:
- Libksba is a library to make the tasks of working with X.509 certificates, CMS data and related objects more easy.
liblbxutil¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- pkgconfig, xproto, xextproto, util-macros
- Description:
- liblbxutil - Low Bandwith X extension (LBX) utility routines.
libmatheval¶
- Homepage:
- Spack package:
- Versions:
- 1.1.11
- Build Dependencies:
- guile
- Description:
- GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. It supports expressions in any number of variables of arbitrary names, decimal and symbolic constants, basic unary and binary operators, and elementary mathematical functions. In addition to parsing and evaluation, libmatheval can also compute symbolic derivatives and output expressions to strings.
libmesh¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- petsc, mpi
- Link Dependencies:
- petsc, mpi
- Description:
- The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms.
libmng¶
- Homepage:
- Spack package:
- Versions:
- 2.0.3, 2.0.2
- Build Dependencies:
- zlib, jpeg, lcms
- Link Dependencies:
- zlib, jpeg, lcms
- Description:
- libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format.
libmongoc¶
- Homepage:
- Spack package:
- Versions:
- 1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1
- Build Dependencies:
- autoconf, m4, openssl, libtool, automake, libbson, zlib, snappy
- Link Dependencies:
- zlib, libbson, openssl, snappy
- Description:
- libmongoc is a client library written in C for MongoDB.
libmonitor¶
- Homepage:
- Spack package:
- Versions:
- 20130218
- Description:
- Libmonitor is a library for process and thread control.
libnbc¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- LibNBC is a prototypic implementation of a nonblocking interface for MPI collective operations. Based on ANSI C and MPI-1, it supports all MPI-1 collective operations in a nonblocking manner. LibNBC is distributed under the BSD license.
libogg¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Description:
- Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
liboldx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- X version 10 backwards compatibility.
libpcap¶
- Homepage:
- Spack package:
- Versions:
- 1.8.1
- Description:
- libpcap is a portable library in C/C++ for packet capture
libpciaccess¶
- Homepage:
- Spack package:
- Versions:
- 0.13.5, 0.13.4
- Build Dependencies:
- pkgconfig, libtool, util-macros
- Description:
- Generic PCI access library.
libpfm4¶
- Homepage:
- Spack package:
- Versions:
- 4.8.0
- Description:
- libpfm4 is a userspace library to help setup performance events for use with the perf_events Linux kernel interface.
libpipeline¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2
- Build Dependencies:
- pkgconfig
- Description:
- libpipeline is a C library for manipulating pipelines of subprocesses in a flexible and convenient way.
libpng¶
- Homepage:
- Spack package:
- Versions:
- 1.6.29, 1.6.27, 1.2.57
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- libpng is the official PNG reference library.
libpsl¶
- Homepage:
- Spack package:
- Versions:
- 0.17.0
- Build Dependencies:
- pkgconfig, python, icu4c, gettext
- Link Dependencies:
- icu4c
- Test Dependencies:
- valgrind
- Description:
- libpsl - C library to handle the Public Suffix List.
libpthread-stubs¶
- Homepage:
- Spack package:
- Versions:
- 0.4, 0.3
- Description:
- The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default.
libquo¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.3, 1.2.9
- Build Dependencies:
- automake, autoconf, libtool, mpi
- Link Dependencies:
- mpi
- Description:
- QUO (as in "status quo") is a runtime library that aids in accommodating thread-level heterogeneity in dynamic, phased MPI+X applications comprising single- and multi-threaded libraries.
libsigsegv¶
- Homepage:
- Spack package:
- Versions:
- 2.11, 2.10
- Description:
- GNU libsigsegv is a library for handling page faults in user mode.
libsm¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, xproto, xtrans, libice, util-macros
- Link Dependencies:
- libice
- Description:
- libSM - X Session Management Library.
libsodium¶
- Homepage:
- Spack package:
- Versions:
- 1.0.15, 1.0.13, 1.0.12, 1.0.11, 1.0.10, 1.0.3, 1.0.2, 1.0.1, 1.0.0, 0.7.1
- Description:
- Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
libsplash¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.6.0, 1.5.0, 1.4.0, 1.3.1, 1.2.4, master
- Build Dependencies:
- hdf5, cmake, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- libSplash aims at developing a HDF5-based I/O library for HPC simulations. It is created as an easy-to-use frontend for the standard HDF5 library with support for MPI processes in a cluster environment. While the standard HDF5 library provides detailed low-level control, libSplash simplifies tasks commonly found in large-scale HPC simulations, such as iterative computations and MPI distributed processes.
libssh2¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0, 1.7.0, 1.4.3
- Build Dependencies:
- cmake, openssl, zlib, xz
- Link Dependencies:
- zlib, openssl, xz
- Description:
- libssh2 is a client-side C library implementing the SSH2 protocol
libsvm¶
- Homepage:
- Spack package:
- Versions:
- 322
- Description:
- Libsvm is a simple, easy-to-use, and efficient software for SVM classification and regression.
libszip¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1, 2.1
- Description:
- Szip is an implementation of the extended-Rice lossless compression algorithm. It provides lossless compression of scientific data, and is provided with HDF software products.
libtermkey¶
- Homepage:
- Spack package:
- Versions:
- 0.18, 0.17, 0.16, 0.15b, 0.14
- Build Dependencies:
- ncurses, libtool
- Link Dependencies:
- ncurses
- Description:
- Easy keyboard entry processing for terminal programs
libtiff¶
- Homepage:
- Spack package:
- Versions:
- 4.0.8, 4.0.7, 4.0.6, 4.0.3, 3.9.7
- Build Dependencies:
- zlib, jpeg, xz
- Link Dependencies:
- zlib, jpeg, xz
- Description:
- libtiff graphics format library
libtool¶
- Homepage:
- Spack package:
- Versions:
- 2.4.6, 2.4.2
- Build Dependencies:
- m4
- Description:
- libtool -- library building part of autotools.
libunistring¶
- Homepage:
- Spack package:
- Versions:
- 0.9.7, 0.9.6
- Description:
- This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwind¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Description:
- A portable and efficient C programming interface (API) to determine the call-chain of a program.
libuv¶
- Homepage:
- Spack package:
- Versions:
- 1.9.0
- Build Dependencies:
- automake, autoconf, libtool
- Description:
- Multi-platform library with a focus on asynchronous IO
libvorbis¶
- Homepage:
- Spack package:
- Versions:
- 1.3.5
- Build Dependencies:
- libogg, pkgconfig
- Link Dependencies:
- libogg
- Description:
- Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format for mid to high quality (8kHz- 48.0kHz, 16+ bit, polyphonic) audio and music at fixed and variable bitrates from 16 to 128 kbps/channel.
libvterm¶
- Homepage:
- Spack package:
- Versions:
- 681
- Description:
- An abstract library implementation of a terminal emulator
libwebsockets¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1, 2.1.1, 2.1.0, 2.0.3, 1.7.9
- Build Dependencies:
- zlib, openssl, cmake
- Link Dependencies:
- zlib, openssl
- Description:
- C library for lightweight websocket clients and servers.
libwindowswm¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- windowswmproto, libxext, libx11, util-macros, pkgconfig, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- WindowsWM - Cygwin/X rootless window management extension. WindowsWM is a simple library designed to interface with the Windows-WM extension. This extension allows X window managers to better interact with the Cygwin XWin server when running X11 in a rootless mode.
libx11¶
- Homepage:
- Spack package:
- Versions:
- 1.6.5, 1.6.3
- Build Dependencies:
- xproto, xextproto, util-macros, perl, pkgconfig, kbproto, xtrans, libxcb, inputproto
- Link Dependencies:
- kbproto, xextproto, libxcb
- Description:
- libX11 - Core X11 protocol client library.
libxau¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8
- Build Dependencies:
- pkgconfig, xproto, util-macros
- Link Dependencies:
- xproto
- Description:
- The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.
libxaw¶
- Homepage:
- Spack package:
- Versions:
- 1.0.13
- Build Dependencies:
- xproto, libxext, xextproto, util-macros, libxt, libxpm, libxmu, pkgconfig, libx11
- Link Dependencies:
- libxpm, libxext, libxmu, libx11, libxt
- Description:
- Xaw is the X Athena Widget Set. Xaw is a widget set based on the X Toolkit Intrinsics (Xt) Library.
libxaw3d¶
- Homepage:
- Spack package:
- Versions:
- 1.6.2
- Build Dependencies:
- libxext, libx11, util-macros, libxt, libxpm, libxmu, pkgconfig
- Link Dependencies:
- libxpm, libxext, libxmu, libx11, libxt
- Description:
- Xaw3d is the X 3D Athena Widget Set. Xaw3d is a widget set based on the X Toolkit Intrinsics (Xt) Library.
libxc¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.2.2, 2.2.1
- Description:
- Libxc is a library of exchange-correlation functionals for density- functional theory.
libxcb¶
- Homepage:
- Spack package:
- Versions:
- 1.12, 1.11.1, 1.11
- Build Dependencies:
- libxdmcp, util-macros, xcb-proto, pkgconfig, libxau, libpthread-stubs
- Link Dependencies:
- libxdmcp, libpthread-stubs, libxau
- Description:
- The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libxcomposite¶
- Homepage:
- Spack package:
- Versions:
- 0.4.4
- Build Dependencies:
- libxfixes, compositeproto, libx11, util-macros, pkgconfig, fixesproto
- Link Dependencies:
- libxfixes, libx11
- Description:
- libXcomposite - client library for the Composite extension to the X11 protocol.
libxcursor¶
- Homepage:
- Spack package:
- Versions:
- 1.1.14
- Build Dependencies:
- libxfixes, libxrender, libx11, util-macros, pkgconfig, fixesproto
- Link Dependencies:
- libxfixes, libxrender, libx11
- Description:
- libXcursor - X Window System Cursor management library.
libxdamage¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- libxfixes, xextproto, util-macros, libx11, pkgconfig, damageproto, fixesproto
- Link Dependencies:
- libxfixes, libx11
- Description:
- This package contains the library for the X Damage extension.
libxdmcp¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- pkgconfig, xproto, util-macros
- Description:
- libXdmcp - X Display Manager Control Protocol library.
libxevie¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libxext, xextproto, util-macros, evieext, pkgconfig, xproto, libx11
- Link Dependencies:
- libxext, libx11
- Description:
- Xevie - X Event Interception Extension (XEvIE).
libxext¶
- Homepage:
- Spack package:
- Versions:
- 1.3.3
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros, xextproto
- Link Dependencies:
- libx11
- Description:
- libXext - library for common extensions to the X11 protocol.
libxfixes¶
- Homepage:
- Spack package:
- Versions:
- 5.0.2
- Build Dependencies:
- xproto, xextproto, util-macros, libx11, pkgconfig, fixesproto
- Link Dependencies:
- libx11
- Description:
- This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate.
libxfont¶
- Homepage:
- Spack package:
- Versions:
- 1.5.2
- Build Dependencies:
- xproto, freetype, util-macros, pkgconfig, xtrans, libfontenc, fontsproto
- Link Dependencies:
- libfontenc, freetype
- Description:
- libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new API's in libXft, or the legacy API's in libX11.
libxfont2¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- xproto, freetype, util-macros, pkgconfig, xtrans, libfontenc, fontsproto
- Link Dependencies:
- libfontenc, freetype
- Description:
- libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new API's in libXft, or the legacy API's in libX11.
libxfontcache¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- libxext, libx11, util-macros, fontcacheproto, pkgconfig, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- Xfontcache - X-TrueType font cache extension client library.
libxft¶
- Homepage:
- Spack package:
- Versions:
- 2.3.2
- Build Dependencies:
- fontconfig, libxrender, freetype, libx11, util-macros, pkgconfig
- Link Dependencies:
- fontconfig, libxrender, freetype, libx11
- Description:
- X FreeType library. Xft version 2.1 was the first stand alone release of Xft, a library that connects X applications with the FreeType font rasterization library. Xft uses fontconfig to locate fonts so it has no configuration files.
libxi¶
- Homepage:
- Spack package:
- Versions:
- 1.7.6
- Build Dependencies:
- libxext, xextproto, xproto, libxfixes, inputproto, libx11
- Link Dependencies:
- libxfixes, libxext, libx11
- Description:
- libXi - library for the X Input Extension.
libxinerama¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- libxext, libx11, util-macros, pkgconfig, xineramaproto, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- libXinerama - API for Xinerama extension to X11 Protocol.
libxkbcommon¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0
- Build Dependencies:
- autoconf, m4, libtool, bison, automake, xkbdata
- Link Dependencies:
- xkbdata
- Description:
- xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications.
libxkbfile¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- pkgconfig, kbproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- XKB file handling routines.
libxkbui¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- pkgconfig, libxkbfile, libx11, util-macros, libxt
- Link Dependencies:
- libxkbfile, libx11, libxt
- Description:
- X.org libxkbui library.
libxml2¶
- Homepage:
- Spack package:
- Versions:
- 2.9.4, 2.9.2, 2.7.8
- Build Dependencies:
- pkgconfig, python, zlib, xz
- Link Dependencies:
- python, zlib, xz
- Description:
- Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.
libxmu¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- libxext, xextproto, util-macros, libxt, pkgconfig, libx11
- Link Dependencies:
- libxext, libx11, libxt
- Description:
- This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt.
libxp¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- printproto, libxext, xextproto, util-macros, pkgconfig, libxau, libx11
- Link Dependencies:
- libxext, libx11, libxau
- Description:
- libXp - X Print Client Library.
libxpm¶
- Homepage:
- Spack package:
- Versions:
- 3.5.12, 3.5.11, 3.5.10, 3.5.9, 3.5.8, 3.5.7
- Build Dependencies:
- pkgconfig, xproto, gettext, libx11, util-macros
- Link Dependencies:
- libx11, gettext
- Description:
- libXpm - X Pixmap (XPM) image file format library.
libxpresent¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- xproto, xextproto, util-macros, libx11, pkgconfig, presentproto
- Link Dependencies:
- libx11
- Description:
- This package contains header files and documentation for the Present extension. Library and server implementations are separate.
libxprintapputil¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- printproto, libxprintutil, libx11, util-macros, pkgconfig, libxau, libxp
- Link Dependencies:
- libxprintutil, libxp, libx11, libxau
- Description:
- Xprint application utility routines.
libxprintutil¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- printproto, libx11, util-macros, libxt, pkgconfig, libxau, libxp
- Link Dependencies:
- libxau, libxp, libx11, libxt
- Description:
- Xprint application utility routines.
libxrandr¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- libxext, randrproto, libxrender, libx11, util-macros, pkgconfig, renderproto, xextproto
- Link Dependencies:
- libxext, libxrender, libx11
- Description:
- libXrandr - X Resize, Rotate and Reflection extension library.
libxrender¶
- Homepage:
- Spack package:
- Versions:
- 0.9.10, 0.9.9
- Build Dependencies:
- pkgconfig, libx11, util-macros, renderproto
- Link Dependencies:
- libx11, renderproto
- Description:
- libXrender - library for the Render Extension to the X11 protocol.
libxres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- libxext, libx11, util-macros, resourceproto, pkgconfig, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- libXRes - X-Resource extension client library.
libxscrnsaver¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- libxext, libx11, util-macros, pkgconfig, scrnsaverproto, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- XScreenSaver - X11 Screen Saver extension client library
libxshmfence¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- pkgconfig, xproto, util-macros
- Description:
- libxshmfence - Shared memory 'SyncFence' synchronization primitive. This library offers a CPU-based synchronization primitive compatible with the X SyncFence objects that can be shared between processes using file descriptor passing.
libxslt¶
- Homepage:
- Spack package:
- Versions:
- 1.1.29, 1.1.28, 1.1.26
- Build Dependencies:
- libgcrypt, xz, zlib, libiconv, libxml2
- Link Dependencies:
- libgcrypt, xz, zlib, libiconv, libxml2
- Description:
- Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOME project. It also implements most of the EXSLT set of processor-portable extensions functions and some of Saxon's evaluate and expressions extensions.
libxsmm¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.8.3, 1.8.2, 1.8.1, 1.8, 1.7.1, 1.7, 1.6.6, 1.6.5, 1.6.4, 1.6.3, 1.6.2, 1.6.1, 1.6, 1.5.2, 1.5.1, 1.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4
- Description:
- Library targeting Intel Architecture for small, dense or sparse matrix multiplications, and small convolutions.
libxstream¶
- Homepage:
- Spack package:
- Versions:
- 0.9.0
- Description:
- LIBXSTREAM is a library to work with streams, events, and code regions that are able to run asynchronous while preserving the usual stream conditions.
libxt¶
- Homepage:
- Spack package:
- Versions:
- 1.1.5
- Build Dependencies:
- xproto, libx11, libsm, pkgconfig, kbproto, libice, util-macros
- Link Dependencies:
- libx11, libsm, libice
- Description:
- libXt - X Toolkit Intrinsics library.
libxtrap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- libxext, xextproto, util-macros, libxt, pkgconfig, trapproto, libx11
- Link Dependencies:
- libxext, libx11, libxt
- Description:
- libXTrap is the Xlib-based client API for the DEC-XTRAP extension. XTrap was a proposed standard extension for X11R5 which facilitated the capturing of server protocol and synthesizing core input events. Digital participated in the X Consortium's xtest working group which chose to evolve XTrap functionality into the XTEST & RECORD extensions for X11R6. As X11R6 was released in 1994, XTrap has now been deprecated for over 15 years, and uses of it should be quite rare.
libxtst¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- libxext, libx11, xextproto, recordproto, libxi, pkgconfig, inputproto, util-macros, fixesproto
- Link Dependencies:
- libxext, libx11, libxi
- Description:
- libXtst provides the Xlib-based client API for the XTEST & RECORD extensions. The XTEST extension is a minimal set of client and server extensions required to completely test the X11 server with no user intervention. This extension is not intended to support general journaling and playback of user actions. The RECORD extension supports the recording and reporting of all core X protocol and arbitrary X extension protocol.
libxv¶
- Homepage:
- Spack package:
- Versions:
- 1.0.10
- Build Dependencies:
- libxext, libx11, util-macros, pkgconfig, videoproto, xextproto
- Link Dependencies:
- libxext, libx11
- Description:
- libXv - library for the X Video (Xv) extension to the X Window System.
libxvmc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- libxext, libxv, libx11, util-macros, pkgconfig, videoproto, xextproto
- Link Dependencies:
- libxext, libxv, libx11
- Description:
- X.org libXvMC library.
libxxf86dga¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- libxext, xf86dgaproto, xextproto, util-macros, xproto, pkgconfig, libx11
- Link Dependencies:
- libxext, libx11
- Description:
- libXxf86dga - Client library for the XFree86-DGA extension.
libxxf86misc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libxext, xextproto, util-macros, xf86miscproto, pkgconfig, xproto, libx11
- Link Dependencies:
- libxext, libx11
- Description:
- libXxf86misc - Extension library for the XFree86-Misc X extension.
libxxf86vm¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- libxext, xextproto, util-macros, xproto, pkgconfig, xf86vidmodeproto, libx11
- Link Dependencies:
- libxext, libx11
- Description:
- libXxf86vm - Extension library for the XFree86-VidMode X extension.
libyogrt¶
- Homepage:
- Spack package:
- Versions:
- 1.20-6, 1.20-5, 1.20-4, 1.20-3, 1.20-2
- Description:
- Your One Get Remaining Time Library.
libzip¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Description:
- libzip is a C library for reading, creating, and modifying zip archives.
likwid¶
- Homepage:
- Spack package:
- Versions:
- 4.3.0, 4.2.1, 4.2.0, 4.1.2
- Build Dependencies:
- perl, lua
- Link Dependencies:
- lua
- Run Dependencies:
- perl
- Description:
- Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. It works for Intel and AMD processors on the Linux operating system.
linkphase3¶
- Homepage:
- Spack package:
- Versions:
- 2017-06-14
- Description:
- Haplotype reconstruction in pedigreed populations.
listres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- xproto, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libxt
- Description:
- The listres program generates a list of X resources for a widget in an X client written using a toolkit based on libXt.
llvm¶
- Homepage:
- Spack package:
- Versions:
- 5.0.1, 5.0.0, 4.0.1, 4.0.0, 3.9.1, 3.9.0, 3.8.1, 3.8.0, 3.7.1, 3.7.0, 3.6.2, 3.5.1, 3.0, trunk
- Build Dependencies:
- ncurses, python, isl, swig, libedit, py-lit, binutils, cmake, gmp
- Link Dependencies:
- ncurses, isl, swig, libedit, binutils, python, gmp
- Run Dependencies:
- py-lit
- Description:
- The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name "LLVM" itself is not an acronym; it is the full name of the project.
llvm-lld¶
- Homepage:
- Spack package:
- Versions:
- 3.4
- Build Dependencies:
- llvm, cmake
- Link Dependencies:
- llvm
- Description:
- lld - The LLVM Linker lld is a new set of modular code for creating linker tools.
llvm-openmp-ompt¶
- Homepage:
- Spack package:
- Versions:
- 3.9.2b2, 3.9.2b, towards_tr4
- Build Dependencies:
- ninja, llvm, cmake
- Link Dependencies:
- llvm
- Description:
- The OpenMP subproject provides an OpenMP runtime for use with the OpenMP implementation in Clang. This branch includes experimental changes for OMPT, the OpenMP Tools interface
lmdb¶
- Homepage:
- Spack package:
- Versions:
- 0.9.21, 0.9.16
- Description:
- Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
lmod¶
- Homepage:
- Spack package:
- Versions:
- 7.7.13, 7.7, 7.6.14, 7.4.11, 7.4.10, 7.4.9, 7.4.8, 7.4.5, 7.4.1, 7.3, 6.4.5, 6.4.1, 6.3.7, 6.0.1
- Build Dependencies:
- lua-luaposix, tcl, lua, lua-luafilesystem
- Link Dependencies:
- lua
- Run Dependencies:
- lua-luaposix, tcl, lua-luafilesystem
- Description:
- Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users' environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found.
lndir¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- pkgconfig, xproto
- Description:
- lndir - create a shadow directory of symbolic links to another directory tree.
log4cplus¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- cmake
- Description:
- log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily granular control over log management and configuration.
log4cxx¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0
- Build Dependencies:
- apr-util, libxml2
- Link Dependencies:
- apr-util, libxml2
- Description:
- A C++ port of Log4j
lrslib¶
- Homepage:
- Spack package:
- Versions:
- 6.2, 6.1, 6.0, 5.1, 4.3
- Build Dependencies:
- libtool, gmp
- Link Dependencies:
- gmp
- Description:
- lrslib Ver 6.2 is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems and comes with a choice of three arithmetic packages
lrzip¶
- Homepage:
- Spack package:
- Versions:
- 0.630, 0.621, 0.616, 0.615, master
- Build Dependencies:
- zlib, lzo, bzip2
- Link Dependencies:
- zlib, lzo, bzip2
- Description:
- A compression utility that excels at compressing large files (usually > 10-50 MB). Larger files and/or more free RAM means that the utility will be able to more effectively compress your files (ie: faster / smaller size), especially if the filesize(s) exceed 100 MB. You can either choose to optimise for speed (fast compression / decompression) or size, but not both.
lua¶
- Homepage:
- Spack package:
- Versions:
- 5.3.4, 5.3.2, 5.3.1, 5.3.0, 5.2.4, 5.2.3, 5.2.2, 5.2.1, 5.2.0, 5.1.5, 5.1.4, 5.1.3
- Build Dependencies:
- ncurses, readline
- Link Dependencies:
- ncurses, readline
- Description:
- The Lua programming language interpreter and library.
lua-bitlib¶
- Homepage:
- Spack package:
- Versions:
- 23
- Build Dependencies:
- lua
- Link Dependencies:
- lua
- Description:
- Lua-jit-like bitwise operations for lua
lua-lpeg¶
- Homepage:
- Spack package:
- Versions:
- 0.12.1
- Build Dependencies:
- lua
- Link Dependencies:
- lua
- Description:
- pattern-matching for lua
lua-luafilesystem¶
- Homepage:
- Spack package:
- Versions:
- 1_6_3
- Build Dependencies:
- lua, git
- Link Dependencies:
- lua
- Description:
- LuaFileSystem is a Lua library developed to complement the set of functions related to file systems offered by the standard Lua distribution. LuaFileSystem offers a portable way to access the underlying directory structure and file attributes. LuaFileSystem is free software and uses the same license as Lua 5.1
lua-luaposix¶
- Homepage:
- Spack package:
- Versions:
- 33.4.0
- Build Dependencies:
- lua
- Link Dependencies:
- lua
- Description:
- Lua posix bindings, including ncurses
lua-mpack¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0-0
- Build Dependencies:
- lua, msgpack-c
- Link Dependencies:
- lua, msgpack-c
- Description:
- lua bindings to libmpack
luit¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- pkgconfig, libfontenc, libx11, util-macros
- Link Dependencies:
- libfontenc, libx11
- Description:
- Luit is a filter that can be run between an arbitrary application and a UTF-8 terminal emulator such as xterm. It will convert application output from the locale's encoding into UTF-8, and convert terminal input from UTF-8 into the locale's encoding.
lulesh¶
- Homepage:
- Spack package:
- Versions:
- 2.0.3
- Build Dependencies:
- silo, hdf5, mpi
- Link Dependencies:
- silo, hdf5, mpi
- Description:
- LULESH is a highly simplified application, hard-coded to only style typical in scientific C or C++ based applications. Hard code to only solve a Sedov blast problem with analytic answer
lumpy-sv¶
- Homepage:
- Spack package:
- Versions:
- 0.2.13
- Build Dependencies:
- htslib
- Link Dependencies:
- htslib
- Description:
- A probabilistic framework for structural variant discovery.
lwgrp¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Thie light-weight group library provides process group representations using O(log N) space and time.
lwm2¶
- Homepage:
- Spack package:
- Versions:
- torus
- Build Dependencies:
- papi, mpi
- Link Dependencies:
- papi, mpi
- Description:
- LWM2: Light Weight Measurement Module. This is a PMPI module that can collect a number of time-sliced MPI and POSIX I/O measurements from a program.
lz4¶
- Homepage:
- Spack package:
- Versions:
- 1.8.1.2, 1.7.5, 1.3.1
- Description:
- LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.
lzma¶
- Homepage:
- Spack package:
- Versions:
- 4.32.7
- Description:
- LZMA Utils are legacy data compression software with high compression ratio. LZMA Utils are no longer developed, although critical bugs may be fixed as long as fixing them doesn't require huge changes to the code. Users of LZMA Utils should move to XZ Utils. XZ Utils support the legacy .lzma format used by LZMA Utils, and can also emulate the command line tools of LZMA Utils. This should make transition from LZMA Utils to XZ Utils relatively easy.
lzo¶
- Homepage:
- Spack package:
- Versions:
- 2.09, 2.08, 2.07, 2.06, 2.05
- Description:
- Real-time data compression library
m4¶
- Homepage:
- Spack package:
- Versions:
- 1.4.18, 1.4.17
- Build Dependencies:
- libsigsegv
- Link Dependencies:
- libsigsegv
- Description:
- GNU M4 is an implementation of the traditional Unix macro processor.
macsio¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- json-cwx, silo, hdf5, exodusii, typhonio, mpi, cmake, scr
- Link Dependencies:
- json-cwx, silo, hdf5, exodusii, typhonio, mpi, scr
- Description:
- A Multi-purpose, Application-Centric, Scalable I/O Proxy Application
mad-numdiff¶
- Homepage:
- Spack package:
- Versions:
- develop, 20150724
- Build Dependencies:
- cmake
- Description:
- compare unformatted text files with numerical content
mafft¶
- Homepage:
- Spack package:
- Versions:
- 7.221
- Description:
- MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.
magics¶
- Homepage:
- Spack package:
- Versions:
- 2.34.3, 2.34.1, 2.33.0, 2.32.0, 2.31.0, 2.29.6, 2.29.4, 2.29.0
- Build Dependencies:
- libpng, py-numpy, perl-xml-parser, zlib, pkgconfig, grib-api, qt, eccodes, cmake, netcdf-cxx, perl, expat, boost, proj, pango, libemos, swig, python
- Link Dependencies:
- libpng, eccodes, zlib, grib-api, qt, netcdf-cxx, boost, proj, pango, libemos, expat, python
- Run Dependencies:
- py-numpy, python
- Description:
- Magics is the latest generation of the ECMWF's Meteorological plotting software MAGICS. Although completely redesigned in C++, it is intended to be as backwards-compatible as possible with the Fortran interface.
magma¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- lapack, cuda, cmake
- Link Dependencies:
- lapack, cuda
- Description:
- The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current "Multicore+GPU" systems.
makedepend¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, xproto
- Description:
- makedepend - create dependencies in makefiles.
mallocmc¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.2.0crp, 2.1.0crp, 2.0.1crp, 2.0.0crp, 1.0.2crp, master
- Build Dependencies:
- cmake
- Link Dependencies:
- cuda, boost
- Description:
- mallocMC: Memory Allocator for Many Core Architectures. This project provides a framework for fast memory managers on many core accelerators. Currently, it supports NVIDIA GPUs of compute capability sm_20 or higher through the ScatterAlloc algorithm. mallocMC is header-only, but requires a few other C++ libraries to be available.
man-db¶
- Homepage:
- Spack package:
- Versions:
- 2.7.6.1
- Build Dependencies:
- autoconf, libpipeline, gettext, flex, automake, bzip2, groff, lzma, xz
- Link Dependencies:
- autoconf, libpipeline, gettext, flex, automake, bzip2, groff, lzma, xz
- Run Dependencies:
- xz, lzma, groff, bzip2
- Description:
- man-db is an implementation of the standard Unix documentation system accessed using the man command. It uses a Berkeley DB database in place of the traditional flat-text whatis databases.
maq¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1, 0.5.0
- Description:
- Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.
mariadb¶
- Homepage:
- Spack package:
- Versions:
- 10.2.8, 10.1.23, 10.1.14, 5.5.56, 5.5.49
- Build Dependencies:
- ncurses, libaio, zlib, boost, libedit, cmake, jemalloc, libevent
- Link Dependencies:
- ncurses, libaio, zlib, boost, libedit, libevent, jemalloc
- Description:
- MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop- in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for a wide variety of use cases.
masa¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- autoconf, libtool, metaphysicl, swig, automake, python
- Link Dependencies:
- python, metaphysicl
- Description:
- MASA (Manufactured Analytical Solution Abstraction) is a library written in C++ (with C, python and Fortran90 interfaces) which provides a suite of manufactured solutions for the software verification of partial differential equation solvers in multiple dimensions.
masurca¶
- Homepage:
- Spack package:
- Versions:
- 3.2.3
- Build Dependencies:
- perl, zlib, boost
- Link Dependencies:
- zlib, boost
- Run Dependencies:
- perl
- Description:
- MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches.
matio¶
- Homepage:
- Spack package:
- Versions:
- 1.5.9, 1.5.2
- Build Dependencies:
- hdf5, zlib
- Link Dependencies:
- hdf5, zlib
- Description:
- matio is an C library for reading and writing Matlab MAT files
matlab¶
- Homepage:
- Spack package:
- Versions:
- R2016b
- Description:
- MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python. Note: MATLAB is licensed software. You will need to create an account on the MathWorks homepage and download MATLAB yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
maven¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0, 3.3.9
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Apache Maven is a software project management and comprehension tool.
maverick¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Description:
- MavericK is a program for inferring population structure on the basis of genetic information.
mawk¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4
- Description:
- mawk is an interpreter for the AWK Programming Language.
mbedtls¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0, 2.2.1, 2.2.0, 2.1.4, 2.1.3, 1.3.16
- Build Dependencies:
- cmake
- Description:
- mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint.
mcl¶
- Homepage:
- Spack package:
- Versions:
- 14-137
- Description:
- The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.
mdtest¶
- Homepage:
- Spack package:
- Versions:
- 1.9.3
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/close operations on files and directories and then reports the performance.
meep¶
- Homepage:
- Spack package:
- Versions:
- 1.3, 1.2.1, 1.1.1
- Build Dependencies:
- hdf5, mpi, lapack, harminv, libctl, gsl, guile, blas
- Link Dependencies:
- hdf5, mpi, lapack, harminv, libctl, gsl, guile, blas
- Description:
- Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
mefit¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- py-numpy, casper, jellyfish, py-htseq
- Link Dependencies:
- py-numpy, casper, jellyfish, py-htseq
- Description:
- This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality.
memaxes¶
- Homepage:
- Spack package:
- Versions:
- 0.5
- Build Dependencies:
- qt, cmake
- Link Dependencies:
- qt
- Description:
- MemAxes is a visualizer for sampled memory trace data.
meme¶
- Homepage:
- Spack package:
- Versions:
- 4.12.0, 4.11.4
- Build Dependencies:
- perl, python, mpi
- Link Dependencies:
- libxslt, libgcrypt, libxml2, zlib, mpi
- Run Dependencies:
- perl, python
- Description:
- The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
meraculous¶
- Homepage:
- Spack package:
- Versions:
- 2.2.4
- Build Dependencies:
- gnuplot, perl, perl-log-log4perl, cmake, boost
- Link Dependencies:
- gnuplot, boost
- Run Dependencies:
- perl, perl-log-log4perl
- Description:
- Meraculous is a while genome assembler for Next Generation Sequencing data geared for large genomes.
mercurial¶
- Homepage:
- Spack package:
- Versions:
- 4.4.1, 4.1.2, 3.9.1, 3.9, 3.8.4, 3.8.3, 3.8.2, 3.8.1
- Build Dependencies:
- python, py-docutils, py-pygments, py-certifi
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pygments, py-certifi
- Description:
- Mercurial is a free, distributed source control management tool.
mesa¶
- Homepage:
- Spack package:
- Versions:
- 17.2.3, 17.2.2, 17.1.5, 17.1.4, 17.1.3, 17.1.1, 13.0.6, 12.0.6, 12.0.3
- Build Dependencies:
- libdrm, glproto, flex, libxfixes, bison, libxext, openssl, py-mako, icu4c, libx11, libpthread-stubs, expat, libelf, libxdamage, libxv, llvm, gettext, xproto, pkgconfig, binutils, libxcb, libxshmfence, libxvmc, dri2proto, python, dri3proto, presentproto
- Link Dependencies:
- libdrm, libxdamage, libxv, llvm, gettext, glproto, xproto, libxfixes, libx11, libelf, libxext, openssl, presentproto, icu4c, libxvmc, libpthread-stubs, expat, libxcb, libxshmfence
- Description:
- Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
mesa-glu¶
- Homepage:
- Spack package:
- Versions:
- 9.0.0
- Build Dependencies:
- mesa
- Link Dependencies:
- mesa
- Description:
- This package provides the Mesa OpenGL Utility library.
meshkit¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- netgen, moab, cgm, mpi
- Link Dependencies:
- netgen, moab, cgm, mpi
- Description:
- MeshKit is an open-source library of mesh generation functionality. Its design philosophy is two-fold: it provides a collection of meshing algorithms for use in real meshing problems, along with other tools commonly needed to support mesh generation
meson¶
- Homepage:
- Spack package:
- Versions:
- 0.42.0, 0.41.2, 0.41.1
- Build Dependencies:
- ninja, python
- Link Dependencies:
- python
- Run Dependencies:
- ninja, python
- Description:
- Meson is a portable open source build system meant to be both extremely fast, and as user friendly as possible.
mesquite¶
- Homepage:
- Spack package:
- Versions:
- 2.99, 2.3.0, 2.2.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Mesquite (Mesh Quality Improvement Toolkit) is designed to provide a stand-alone, portable, comprehensive suite of mesh quality improvement algorithms and components that can be used to construct custom quality improvement algorithms. Mesquite provides a robust and effective mesh improvement toolkit that allows both meshing researchers application scientists to benefit from the latest developments in mesh quality control and improvement.
metaphysicl¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- automake, autoconf, libtool
- Description:
- Metaprogramming and operator-overloaded classes for numerical simulations.
metasv¶
- Homepage:
- Spack package:
- Versions:
- 0.5.4
- Build Dependencies:
- py-pysam, py-pybedtools, py-pyvcf, python
- Link Dependencies:
- python
- Run Dependencies:
- py-pysam, py-pybedtools, py-pyvcf, python
- Description:
- An accurate and integrative structural-variant caller for next generation sequencing
metis¶
- Homepage:
- Spack package:
- Versions:
- 5.1.0, 5.0.2, 4.0.3
- Build Dependencies:
- cmake
- Description:
- METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
mfem¶
- Homepage:
- Spack package:
- Versions:
- 3.3.2, 3.3, 3.2, 3.1, laghos-v1.0
- Build Dependencies:
- netcdf, hypre, metis, hdf5, zlib, sundials, lapack, parmetis, suite-sparse, libunwind, petsc, superlu-dist, mpi, mpfr, blas
- Link Dependencies:
- netcdf, hypre, metis, hdf5, zlib, sundials, lapack, parmetis, suite-sparse, libunwind, petsc, superlu-dist, mpi, mpfr, blas
- Description:
- Free, lightweight, scalable C++ library for finite element methods.
microbiomeutil¶
- Homepage:
- Spack package:
- Versions:
- 20110519
- Build Dependencies:
- perl, cdbfasta, blast-plus
- Link Dependencies:
- cdbfasta, blast-plus
- Run Dependencies:
- perl
- Description:
- Microbiome analysis utilities
minced¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.
miniaero¶
- Homepage:
- Spack package:
- Versions:
- 2016-11-11
- Build Dependencies:
- kokkos
- Link Dependencies:
- kokkos
- Description:
- Proxy Application. MiniAero is a mini-application for the evaulation of programming models and hardware for next generation platforms.
miniamr¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. 3D stencil calculation with Adaptive Mesh Refinement (AMR)
miniconda2¶
- Homepage:
- Spack package:
- Versions:
- 4.3.30, 4.3.14, 4.3.11
- Description:
- The minimalist bootstrap toolset for conda and Python2.
miniconda3¶
- Homepage:
- Spack package:
- Versions:
- 4.3.30, 4.3.14, 4.3.11
- Description:
- The minimalist bootstrap toolset for conda and Python3.
minife¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Build Dependencies:
- qthreads, mpi
- Link Dependencies:
- qthreads, mpi
- Description:
- Proxy Application. MiniFE is an proxy application for unstructured implicit finite element codes.
minighost¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. A Finite Difference proxy application which implements a difference stencil across a homogenous three dimensional domain.
minigmg¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- miniGMG is a compact benchmark for understanding the performance challenges associated with geometric multigrid solvers found in applications built from AMR MG frameworks like CHOMBO or BoxLib when running on modern multi- and manycore-based supercomputers. It includes both productive reference examples as well as highly-optimized implementations for CPUs and GPUs. It is sufficiently general that it has been used to evaluate a broad range of research topics including PGAS programming models and algorithmic tradeoffs inherit in multigrid. miniGMG was developed under the CACHE Joint Math-CS Institute. Note, miniGMG code has been supersceded by HPGMG.
minimap2¶
- Homepage:
- Spack package:
- Versions:
- 2.2
- Build Dependencies:
- py-mappy
- Run Dependencies:
- py-mappy
- Description:
- Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
minimd¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. A simple proxy for the force computations in a typical molecular dynamics applications.
miniqmc¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- lapack, cmake, mpi
- Link Dependencies:
- lapack, mpi
- Description:
- a simplified real space QMC code for algorithm development, performance portability testing, and computer science experiments
minisign¶
- Homepage:
- Spack package:
- Versions:
- 0.7
- Build Dependencies:
- cmake, libsodium
- Link Dependencies:
- libsodium
- Description:
- Minisign is a dead simple tool to sign files and verify signatures.
minismac2d¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. Solves the finite-differenced 2D incompressible Navier-Stokes equations with Spalart-Allmaras one-equation turbulence model on a structured body conforming grid.
minitri¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- A simple, triangle-based data analytics proxy application.
minixyce¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. A portable proxy of some of the key capabilities in the electrical modeling Xyce.
mira¶
- Homepage:
- Spack package:
- Versions:
- 4.0.2
- Build Dependencies:
- expat, boost, gperftools
- Link Dependencies:
- expat, boost, gperftools
- Description:
- MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects.
mirdeep¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0.8
- Build Dependencies:
- perl, viennarna, perl-pdf-api2, squid, randfold, bowtie
- Link Dependencies:
- randfold, viennarna, squid, bowtie
- Run Dependencies:
- perl, perl-pdf-api2
- Description:
- miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
mitofates¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- libsvm
- Link Dependencies:
- libsvm
- Description:
- MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.
mitos¶
- Homepage:
- Spack package:
- Versions:
- 0.9.2, 0.9.1
- Build Dependencies:
- cmake, dyninst, hwloc, mpi
- Link Dependencies:
- dyninst, hwloc, mpi
- Description:
- Mitos is a library and a tool for collecting sampled memory performance data to view with MemAxes
mkfontdir¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- pkgconfig, util-macros
- Run Dependencies:
- mkfontscale
- Description:
- mkfontdir creates the fonts.dir files needed by the legacy X server core font system. The current implementation is a simple wrapper script around the mkfontscale program, which must be built and installed first.
mkfontscale¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- pkgconfig, xproto, libfontenc, freetype, util-macros
- Link Dependencies:
- libfontenc, freetype
- Description:
- mkfontscale creates the fonts.scale and fonts.dir index files used by the legacy X11 font system.
mlhka¶
- Homepage:
- Spack package:
- Versions:
- 2.1
- Description:
- A maximum likelihood ratio test of natural selection, using polymorphism and divergence data.
moab¶
- Homepage:
- Spack package:
- Versions:
- 5.0.0, 4.9.2, 4.9.1, 4.9.0, 4.8.2
- Build Dependencies:
- netcdf, metis, hdf5, mpi, parmetis, parallel-netcdf, zoltan, cgm, blas
- Link Dependencies:
- netcdf, metis, hdf5, mpi, parmetis, parallel-netcdf, zoltan, cgm, blas
- Description:
- MOAB is a component for representing and evaluating mesh data. MOAB can store structured and unstructured mesh, consisting of elements in the finite element 'zoo.' The functional interface to MOAB is simple yet powerful, allowing the representation of many types of metadata commonly found on the mesh. MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than through individual entities, while also versatile enough to support individual entity access.
molcas¶
- Homepage:
- Spack package:
- Versions:
- 8.2
- Build Dependencies:
- cmake, openblas, openmpi, hdf5
- Link Dependencies:
- openblas, openmpi, hdf5
- Description:
- Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. Please set the path to licence file with the following command export MOLCAS_LICENSE=/path/to/molcas/license/
mono¶
- Homepage:
- Spack package:
- Versions:
- 5.4.0.167, 5.0.1.1, 4.8.0.524
- Build Dependencies:
- perl, cmake, libiconv
- Link Dependencies:
- libiconv
- Description:
- Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
mosh¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2, 1.3.0, 1.2.6
- Build Dependencies:
- zlib, ncurses, openssl, protobuf
- Link Dependencies:
- zlib, ncurses, openssl, protobuf
- Run Dependencies:
- perl
- Description:
- Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes. Mosh is a replacement for SSH. It's more robust and responsive, especially over Wi-Fi, cellular, and long-distance links.
mothur¶
- Homepage:
- Spack package:
- Versions:
- 1.39.5
- Build Dependencies:
- boost, readline, mpi
- Link Dependencies:
- boost, readline, mpi
- Description:
- This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
motif¶
- Homepage:
- Spack package:
- Versions:
- 2.3.8
- Build Dependencies:
- libxext, flex, libxft, libxcomposite, libxfixes, libxt, xbitmaps, libx11
- Link Dependencies:
- libxext, flex, libxft, libxcomposite, libxfixes, libxt, xbitmaps, libx11
- Description:
- " Motif - Graphical user interface (GUI) specification and the widget toolkit
motioncor2¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4, 1.0.2, 1.0.1, 1.0.0
- Run Dependencies:
- cuda, libtiff
- Description:
- MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recorded on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level, suitable for both single-particle and tomographic images. MotionCor2 is sufficiently fast to keep up with automated data collection.
mozjs¶
- Homepage:
- Spack package:
- Versions:
- 24.2.0, 17.0.0, 1.8.5
- Build Dependencies:
- perl, libffi, nspr, pkgconfig, zlib, python, readline
- Link Dependencies:
- zlib, libffi, nspr, readline
- Description:
- SpiderMonkey is Mozilla's JavaScript engine written in C/C++. It is used in various Mozilla products, including Firefox, and is available under the MPL2.
mpc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3, 1.0.2
- Build Dependencies:
- gmp, mpfr
- Link Dependencies:
- gmp, mpfr
- Description:
- Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.
mpe2¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Message Passing Extensions (MPE): Parallel, shared X window graphics
mpest¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Description:
- MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.
mpfr¶
- Homepage:
- Spack package:
- Versions:
- 3.1.5, 3.1.4, 3.1.3, 3.1.2
- Build Dependencies:
- gmp
- Link Dependencies:
- gmp
- Description:
- The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
mpibash¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- bash, libcircle, mpi
- Link Dependencies:
- bash, libcircle, mpi
- Description:
- Parallel scripting right from the Bourne-Again Shell (Bash)
mpiblast¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST
mpich¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.2, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1, 3.0.4
- Build Dependencies:
- libfabric
- Link Dependencies:
- libfabric
- Description:
- MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
mpifileutils¶
- Homepage:
- Spack package:
- Versions:
- 0.7, 0.6
- Build Dependencies:
- libarchive, dtcmp, libcircle, lwgrp, mpi
- Link Dependencies:
- libarchive, dtcmp, libcircle, lwgrp, mpi
- Description:
- mpiFileUtils is a suite of MPI-based tools to manage large datasets, which may vary from large directory trees to large files. High- performance computing users often generate large datasets with parallel applications that run with many processes (millions in some cases). However those users are then stuck with single-process tools like cp and rm to manage their datasets. This suite provides MPI-based tools to handle typical jobs like copy, remove, and compare for such datasets, providing speedups of up to 20-30x.
mpileaks¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- adept-utils, callpath, mpi
- Link Dependencies:
- adept-utils, callpath, mpi
- Description:
- Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes.
mpip¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1
- Build Dependencies:
- libunwind, libdwarf, libelf, mpi
- Link Dependencies:
- libunwind, libdwarf, libelf, mpi
- Description:
- mpiP: Lightweight, Scalable MPI Profiling
mpir¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.7.0, 2.6.0
- Build Dependencies:
- yasm, autoconf
- Link Dependencies:
- yasm
- Description:
- Multiple Precision Integers and Rationals.
mpix-launch-swift¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- tcl, stc, mpi, swig
- Link Dependencies:
- tcl, stc, mpi
- Description:
- Library that allows a child MPI application to be launched inside a subset of processes in a parent MPI application.
mrbayes¶
- Homepage:
- Spack package:
- Versions:
- 2017-11-22
- Build Dependencies:
- autoconf, m4, libtool, mpi, libbeagle, automake
- Link Dependencies:
- libbeagle, mpi
- Description:
- MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
mrnet¶
- Homepage:
- Spack package:
- Versions:
- 5.0.1-2, 5.0.1, 4.1.0, 4.0.0
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Description:
- The MRNet Multi-Cast Reduction Network.
mrtrix3¶
- Homepage:
- Spack package:
- Versions:
- 2017-09-25
- Build Dependencies:
- py-numpy, fftw, zlib, mesa-glu, qt, libtiff, python, eigen
- Link Dependencies:
- fftw, zlib, qt, libtiff, mesa-glu, eigen
- Run Dependencies:
- py-numpy, python
- Description:
- MRtrix provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density.
msgpack-c¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- cmake
- Description:
- A small, fast binary interchange format convertible to/from JSON
mshadow¶
- Homepage:
- Spack package:
- Versions:
- 20170721, master
- Description:
- MShadow is a lightweight CPU/GPU Matrix/Tensor C++ Template Library. in C++/CUDA.
multitail¶
- Homepage:
- Spack package:
- Versions:
- 6.4.2
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- MultiTail allows you to monitor logfiles and command output in multiple windows in a terminal, colorize, filter and merge.
multiverso¶
- Homepage:
- Spack package:
- Versions:
- 143187, 0.2, master
- Build Dependencies:
- cmake, boost, mpi
- Link Dependencies:
- boost, mpi
- Description:
- Multiverso is a parameter server based framework for training machine learning models on big data with numbers of machines.
mummer¶
- Homepage:
- Spack package:
- Versions:
- 3.23
- Build Dependencies:
- gnuplot, perl
- Link Dependencies:
- gnuplot
- Run Dependencies:
- perl
- Description:
- MUMmer is a system for rapidly aligning entire genomes.
mumps¶
- Homepage:
- Spack package:
- Versions:
- 5.1.1, 5.0.2, 5.0.1
- Build Dependencies:
- metis, parmetis, lapack, scotch, scalapack, mpi, blas
- Link Dependencies:
- metis, parmetis, lapack, scotch, scalapack, mpi, blas
- Description:
- MUMPS: a MUltifrontal Massively Parallel sparse direct Solver
munge¶
- Homepage:
- Spack package:
- Versions:
- 0.5.11
- Build Dependencies:
- libgcrypt, openssl
- Link Dependencies:
- libgcrypt, openssl
- Description:
- MUNGE Uid 'N' Gid Emporium
muscle¶
- Homepage:
- Spack package:
- Versions:
- 3.8.1551
- Description:
- MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.
muster¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0
- Build Dependencies:
- cmake, boost, mpi
- Link Dependencies:
- boost, mpi
- Description:
- The Muster library provides implementations of sequential and parallel K-Medoids clustering algorithms. It is intended as a general framework for parallel cluster analysis, particularly for performance data analysis on systems with very large numbers of processes.
mvapich2¶
- Homepage:
- Spack package:
- Versions:
- 2.3a, 2.2, 2.1, 2.0, 1.9
- Build Dependencies:
- cuda, libpciaccess, bison
- Link Dependencies:
- cuda, libpciaccess
- Description:
- MVAPICH2 is an MPI implementation for Infiniband networks.
mxml¶
- Homepage:
- Spack package:
- Versions:
- 2.10, 2.9, 2.8, 2.7, 2.6, 2.5
- Description:
- Mini-XML is a small XML library that you can use to read and write XML and XML-like data files in your application without requiring large non- standard libraries.
mxnet¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0.post2, 0.10.0.post1, 0.10.0
- Build Dependencies:
- dmlc-core, opencv, openblas, mshadow, ps-lite, nnvm, cudnn, cub
- Link Dependencies:
- dmlc-core, opencv, openblas, mshadow, ps-lite, nnvm, cudnn, cub
- Description:
- MXNet is a deep learning framework designed for both efficiency and flexibility.
nalu¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- openfast, yaml-cpp, trilinos, hypre, tioga, cmake
- Link Dependencies:
- openfast, yaml-cpp, trilinos, tioga, hypre
- Description:
- Nalu: a generalized unstructured massively parallel low Mach flow code designed to support a variety of energy applications of interest (most notably Wind ECP) built on the Sierra Toolkit and Trilinos solver Tpetra/Epetra stack
namd¶
- Homepage:
- Spack package:
- Versions:
- 2.12
- Build Dependencies:
- tcl, intel-mkl, fftw, python, charm
- Link Dependencies:
- tcl, intel-mkl, fftw, python, charm
- Description:
- NAMDis a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nano¶
- Homepage:
- Spack package:
- Versions:
- 2.6.3, 2.6.2
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- Tiny little text editor
nanoflann¶
- Homepage:
- Spack package:
- Versions:
- 1.2.3
- Build Dependencies:
- cmake
- Description:
- a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.
nasm¶
- Homepage:
- Spack package:
- Versions:
- 2.11.06
- Description:
- NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includes a disassembler as well.
nauty¶
- Homepage:
- Spack package:
- Versions:
- 2.6r7
- Build Dependencies:
- autoconf, m4, zlib, libtool, pkgconfig, automake, help2man, gmp
- Link Dependencies:
- zlib, gmp
- Description:
- nauty and Traces are programs for computing automorphism groups of graphsq and digraphs
ncbi-rmblastn¶
- Homepage:
- Spack package:
- Versions:
- 2.2.28
- Description:
- RMBlast search engine for NCBI
nccl¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4-1, 1.3.0-1
- Build Dependencies:
- cuda
- Link Dependencies:
- cuda
- Description:
- Optimized primitives for collective multi-GPU communication.
nccmp¶
- Homepage:
- Spack package:
- Versions:
- 1.8.2.0
- Build Dependencies:
- netcdf
- Link Dependencies:
- netcdf
- Description:
- Compare NetCDF Files
ncdu¶
- Homepage:
- Spack package:
- Versions:
- 1.11, 1.10, 1.9, 1.8, 1.7
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire gaphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.
ncftp¶
- Homepage:
- Spack package:
- Versions:
- 3.2.6
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- NcFTP Client is a set of application programs implementing the File Transfer Protocol.
ncl¶
- Homepage:
- Spack package:
- Versions:
- 6.4.0
- Build Dependencies:
- netcdf, hdf5, udunits2, flex, libxmu, curl, bison, jpeg, szip, gdal, cairo, tcsh, libiconv, hdf, libxaw, libx11
- Link Dependencies:
- netcdf, hdf5, udunits2, flex, libxmu, curl, jpeg, szip, gdal, cairo, tcsh, libiconv, hdf, libxaw, libx11
- Run Dependencies:
- esmf
- Description:
- NCL is an interpreted language designed specifically for scientific data analysis and visualization. Supports NetCDF 3/4, GRIB 1/2, HDF 4/5, HDF- EOD 2/5, shapefile, ASCII, binary. Numerous analysis functions are built-in.
nco¶
- Homepage:
- Spack package:
- Versions:
- 4.6.7, 4.6.6, 4.6.5, 4.6.4, 4.6.3, 4.6.2, 4.6.1, 4.5.5
- Build Dependencies:
- netcdf, udunits2, antlr, flex, gsl, bison, texinfo
- Link Dependencies:
- netcdf, gsl, udunits2, antlr
- Description:
- The NCO toolkit manipulates and analyzes data stored in netCDF- accessible formats
ncurses¶
- Homepage:
- Spack package:
- Versions:
- 6.0, 5.9
- Build Dependencies:
- pkgconfig
- Description:
- The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD curses.
ncview¶
- Homepage:
- Spack package:
- Versions:
- 2.1.7
- Build Dependencies:
- netcdf, libpng, libxaw, udunits2
- Link Dependencies:
- netcdf, libpng, libxaw, udunits2
- Description:
- Simple viewer for NetCDF files.
ndiff¶
- Homepage:
- Spack package:
- Versions:
- 2.00, 1.00
- Description:
- The ndiff tool is a binary utility that compares putatively similar files while ignoring small numeric differernces. This utility is most often used to compare files containing a lot of floating-point numeric data that may be slightly different due to numeric error.
nek5000¶
- Homepage:
- Spack package:
- Versions:
- develop, 17.0
- Build Dependencies:
- visit, mpi
- Link Dependencies:
- visit, mpi
- Description:
- A fast and scalable high-order solver for computational fluid dynamics
nekbone¶
- Homepage:
- Spack package:
- Versions:
- develop, 17.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- NEK5000 emulation software called NEKbone. Nekbone captures the basic structure and user interface of the extensive Nek5000 software. Nek5000 is a high order, incompressible Navier-Stokes solver based on the spectral element method.
nekcem¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- lapack, mpi, python, blas
- Link Dependencies:
- lapack, mpi, python, blas
- Description:
- Spectral-element solver for Maxwell's equations, drift-diffusion equations, and more.
neovim¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1, 0.2.0
- Build Dependencies:
- lua-bitlib, gperf, cmake, lua-lpeg, unibilium, libtermkey, msgpack-c, libuv, lua, libvterm, jemalloc, lua-mpack
- Link Dependencies:
- unibilium, libtermkey, msgpack-c, libuv, lua-bitlib, lua, gperf, libvterm, lua-lpeg, lua-mpack, jemalloc
- Description:
- NeoVim: the future of vim
netcdf¶
- Homepage:
- Spack package:
- Versions:
- 4.4.1.1, 4.4.1, 4.4.0, 4.3.3.1, 4.3.3
- Build Dependencies:
- m4, zlib, mpi, hdf, curl, parallel-netcdf, hdf5
- Link Dependencies:
- hdf5, zlib, parallel-netcdf, hdf, curl, mpi
- Description:
- NetCDF is a set of software libraries and self-describing, machine- independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netcdf-cxx¶
- Homepage:
- Spack package:
- Versions:
- 4.2
- Build Dependencies:
- netcdf
- Link Dependencies:
- netcdf
- Description:
- Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, and are no longer maintained by Unidata. Developers should migrate to current NetCDF C++ bindings, in Spack package netcdf-cxx4.
netcdf-cxx4¶
- Homepage:
- Spack package:
- Versions:
- 4.3.0, 4.2.1
- Build Dependencies:
- netcdf, automake, autoconf, libtool
- Link Dependencies:
- netcdf
- Description:
- C++ interface for NetCDF4
netcdf-fortran¶
- Homepage:
- Spack package:
- Versions:
- 4.4.4, 4.4.3
- Build Dependencies:
- netcdf
- Link Dependencies:
- netcdf
- Description:
- Fortran interface for NetCDF4
netgauge¶
- Homepage:
- Spack package:
- Versions:
- 2.4.6
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Netgauge is a high-precision network parameter measurement tool. It supports benchmarking of many different network protocols and communication patterns. The main focus lies on accuracy, statistical analysis and easy extensibility.
netgen¶
- Homepage:
- Spack package:
- Versions:
- 5.3.1
- Build Dependencies:
- metis, oce, mpi
- Link Dependencies:
- metis, oce, mpi
- Description:
- NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.
netlib-lapack¶
- Homepage:
- Spack package:
- Versions:
- 3.8.0, 3.7.1, 3.7.0, 3.6.1, 3.6.0, 3.5.0, 3.4.2, 3.4.1, 3.4.0, 3.3.1
- Build Dependencies:
- netlib-xblas, cmake, blas
- Link Dependencies:
- netlib-xblas, blas
- Description:
- LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community.
netlib-scalapack¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2, 2.0.1, 2.0.0
- Build Dependencies:
- lapack, mpi, cmake, blas
- Link Dependencies:
- lapack, mpi, blas
- Description:
- ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines
netlib-xblas¶
- Homepage:
- Spack package:
- Versions:
- 1.0.248
- Description:
- XBLAS is a reference implementation for extra precision BLAS. XBLAS is a reference implementation for the dense and banded BLAS routines, along with extended and mixed precision version. Extended precision is only used internally; input and output arguments remain the same as in the existing BLAS. Extra precisions is implemented as double-double (i.e., 128-bit total, 106-bit significand). Mixed precision permits some input/output arguments of different types (mixing real and complex) or precisions (mixing single and double). This implementation is proof of concept, and no attempt was made to optimize performance; performance should be as good as straightforward but careful code written by hand.
nettle¶
- Homepage:
- Spack package:
- Versions:
- 3.3, 3.2, 2.7.1, 2.7
- Build Dependencies:
- m4, gmp
- Link Dependencies:
- gmp
- Description:
- The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.
neuron¶
- Homepage:
- Spack package:
- Versions:
- develop, 7.5, 7.4, 7.3, 7.2
- Build Dependencies:
- autoconf, pkg-config, libtool, bison, flex, automake, mpi, python, ncurses
- Link Dependencies:
- ncurses, python, mpi
- Description:
- NEURON is a simulation environment for modeling individual and networks of neurons. NEURON models individual neurons via the use of sections that are automatically subdivided into individual compartments, instead of requiring the user to manually create compartments. The primary scripting language is hoc but a Python interface is also available.
nextflow¶
- Homepage:
- Spack package:
- Versions:
- 0.25.6, 0.24.1, 0.23.3, 0.21.0, 0.20.1, 0.17.3
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Data-driven computational pipelines
nfft¶
- Homepage:
- Spack package:
- Versions:
- 3.3.2
- Build Dependencies:
- fftw
- Link Dependencies:
- fftw
- Description:
- NFFT is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of arbitrary input size, and of complex data.
nghttp2¶
- Homepage:
- Spack package:
- Versions:
- 1.26.0
- Build Dependencies:
- python, py-setuptools, py-cython
- Run Dependencies:
- python, py-cython
- Description:
- nghttp2 is an implementation of HTTP/2 and its header compression algorithm HPACK in C.
nginx¶
- Homepage:
- Spack package:
- Versions:
- 1.13.8, 1.12.0
- Build Dependencies:
- openssl, pcre, zlib
- Link Dependencies:
- openssl, pcre, zlib
- Description:
- nginx [engine x] is an HTTP and reverse proxy server, a mail proxy server, and a generic TCP/UDP proxy server, originally written by Igor Sysoev.
ngmlr¶
- Homepage:
- Spack package:
- Versions:
- 0.2.5
- Build Dependencies:
- cmake
- Description:
- Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a reference genome with a focus on reads that span structural variations.
ninja¶
- Homepage:
- Spack package:
- Versions:
- 1.8.2, 1.7.2, 1.6.0
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.
ninja-fortran¶
- Homepage:
- Spack package:
- Versions:
- 1.7.2.gcc0ea, 1.7.2.gaad58, 1.7.1.g7ca7f
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Fortran capable fork of ninja.
nlopt¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.4.2
- Build Dependencies:
- py-numpy, matlab, python, octave, swig, cmake, guile
- Link Dependencies:
- matlab, octave, python, guile, swig
- Run Dependencies:
- py-numpy
- Description:
- NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
nmap¶
- Homepage:
- Spack package:
- Versions:
- 7.31, 7.30
- Description:
- Nmap ("Network Mapper") is a free and open source (license) utility for network discovery and security auditing. It also provides ncat an updated nc
nnvm¶
- Homepage:
- Spack package:
- Versions:
- 20170418, master
- Build Dependencies:
- dmlc-core, cmake
- Link Dependencies:
- dmlc-core
- Description:
- nnvm is a modular, decentralized and lightweight part to help build deep learning libraries.
node-js¶
- Homepage:
- Spack package:
- Versions:
- 8.9.1, 7.1.0, 6.3.0, 6.2.2
- Build Dependencies:
- pkgconfig, python, openssl, libtool, icu4c
- Link Dependencies:
- openssl, icu4c
- Description:
- Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine.
notmuch¶
- Homepage:
- Spack package:
- Versions:
- 0.23.7
- Build Dependencies:
- talloc, xapian-core, gmime, zlib
- Link Dependencies:
- talloc, xapian-core, gmime, zlib
- Description:
- Notmuch is a mail indexer. Essentially, is a very thin front end on top of xapian.
npb¶
- Homepage:
- Spack package:
- Versions:
- 3.3.1
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- The NAS Parallel Benchmarks (NPB) are a small set of programs designed to help evaluate the performance of parallel supercomputers. The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive mesh, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes. Reference implementations of NPB are available in commonly-used programming models like MPI and OpenMP (NPB 2 and NPB 3).
npm¶
- Homepage:
- Spack package:
- Versions:
- 3.10.9, 3.10.5
- Build Dependencies:
- node-js
- Run Dependencies:
- node-js
- Description:
- npm: A package manager for javascript.
npth¶
- Homepage:
- Spack package:
- Versions:
- 1.5, 1.4
- Description:
- nPth is a library to provide the GNU Pth API and thus a non-preemptive threads implementation.
nspr¶
- Homepage:
- Spack package:
- Versions:
- 4.13.1
- Build Dependencies:
- perl
- Description:
- Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
numactl¶
- Homepage:
- Spack package:
- Versions:
- 2.0.11
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- NUMA support for Linux
numdiff¶
- Homepage:
- Spack package:
- Versions:
- 5.9.0, 5.8.1
- Build Dependencies:
- gettext, gmp
- Link Dependencies:
- gettext, gmp
- Description:
- Numdiff is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats.
nut¶
- Homepage:
- Spack package:
- Versions:
- serial, openmp
- Build Dependencies:
- random123, cmake
- Link Dependencies:
- random123
- Description:
- NuT is Monte Carlo code for neutrino transport and is a C++ analog to the Haskell McPhD code. NuT is principally aimed at exploring on-node parallelism and performance issues.
nwchem¶
- Homepage:
- Spack package:
- Versions:
- 6.6
- Build Dependencies:
- lapack, scalapack, blas, python, mpi
- Link Dependencies:
- lapack, scalapack, blas, mpi
- Run Dependencies:
- python
- Description:
- High-performance computational chemistry software
ocaml¶
- Homepage:
- Spack package:
- Versions:
- 4.06.0, 4.03.0
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles
oce¶
- Homepage:
- Spack package:
- Versions:
- 0.18.2, 0.18.1, 0.18, 0.17.2, 0.17.1, 0.17, 0.16.1, 0.16
- Build Dependencies:
- cmake, tbb
- Link Dependencies:
- tbb
- Description:
- Open CASCADE Community Edition: patches/improvements/experiments contributed by users over the official Open CASCADE library.
oclint¶
- Homepage:
- Spack package:
- Versions:
- 0.13
- Build Dependencies:
- ninja, llvm, python, subversion, cmake, py-argparse, git
- Link Dependencies:
- llvm
- Description:
- OClint: a static analysis tool for C, C++, and Objective-C code OCLint is a static code analysis tool for improving quality and reducing defects by inspecting C, C++ and Objective-C code and looking for potential problems
oclock¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libxext, libx11, util-macros, libxt, pkgconfig, libxmu, libxkbfile
- Link Dependencies:
- libxext, libxmu, libxkbfile, libx11, libxt
- Description:
- oclock is a simple analog clock using the SHAPE extension to make a round (possibly transparent) window.
octave¶
- Homepage:
- Spack package:
- Versions:
- 4.2.1, 4.2.0, 4.0.2, 4.0.0
- Build Dependencies:
- hdf5, zlib, glpk, pcre, qt, curl, suite-sparse, gnuplot, fftw, freetype, gl2ps, lapack, qhull, readline, llvm, arpack-ng, pkgconfig, qrupdate, fontconfig, fltk, java, image-magick, blas
- Link Dependencies:
- hdf5, zlib, glpk, pcre, qt, curl, suite-sparse, gnuplot, fftw, freetype, gl2ps, lapack, qhull, readline, llvm, arpack-ng, qrupdate, fontconfig, fltk, java, image-magick, blas
- Description:
- GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
octave-optim¶
- Homepage:
- Spack package:
- Versions:
- 1.5.2
- Build Dependencies:
- octave-struct, octave
- Link Dependencies:
- octave-struct, octave
- Run Dependencies:
- octave
- Description:
- Non-linear optimization toolkit for Octave.
octave-splines¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- octave
- Link Dependencies:
- octave
- Run Dependencies:
- octave
- Description:
- Additional spline functions.
octave-struct¶
- Homepage:
- Spack package:
- Versions:
- 1.0.14
- Build Dependencies:
- octave
- Link Dependencies:
- octave
- Run Dependencies:
- octave
- Description:
- Additional structure manipulation functions for Octave.
octopus¶
- Homepage:
- Spack package:
- Versions:
- 6.0, 5.0.1
- Build Dependencies:
- blas, arpack-ng, libxc, fftw, mpi, lapack, scalapack, parmetis, gsl, metis, netcdf-fortran
- Link Dependencies:
- blas, arpack-ng, libxc, fftw, mpi, lapack, scalapack, parmetis, gsl, metis, netcdf-fortran
- Description:
- A real-space finite-difference (time-dependent) density-functional theory code.
of-adios-write¶
- Homepage:
- Spack package:
- Versions:
- develop, 1706, 1612
- Build Dependencies:
- openfoam-com, adios
- Link Dependencies:
- openfoam-com, adios
- Description:
- adios-write supplies additional libraries and function objects for reading/writing OpenFOAM data with ADIOS. This offering is part of the community repository supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004.
ompss¶
- Homepage:
- Spack package:
- Versions:
- 14.10
- Build Dependencies:
- extrae, hwloc, mpi
- Link Dependencies:
- extrae, hwloc, mpi
- Description:
- OmpSs is an effort to integrate features from the StarSs programming model developed by BSC into a single programming model. In particular, our objective is to extend OpenMP with new directives to support asynchronous parallelism and heterogeneity (devices like GPUs). However, it can also be understood as new directives extending other accelerator based APIs like CUDA or OpenCL. Our OmpSs environment is built on top of our Mercurium compiler and Nanos++ runtime system.
ompt-openmp¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- cmake
- Description:
- LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP mirror. This library provides a drop-in replacement of the OpenMP runtimes for GCC, Intel and LLVM/Clang.
ont-albacore¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2, 1.2.4, 1.1.0
- Build Dependencies:
- py-numpy, py-dateutil, py-pip, py-ont-fast5-api, py-setuptools, py-h5py, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-dateutil, py-ont-fast5-api, py-setuptools, py-h5py, python
- Description:
- Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms. It can be run from the command line on Windows and multiple Linux platforms. A selection of configuration files allow basecalling DNA libraries made with our current range of sequencing kits and Flow Cells.
opa-psm2¶
- Homepage:
- Spack package:
- Versions:
- 10.3-37, 10.3-17, 10.3-10, 10.3-8, 10.2-260, 10.2-235, 10.2-175
- Build Dependencies:
- numactl
- Link Dependencies:
- numactl
- Description:
- Intel Omni-Path Performance Scaled Messaging 2 (PSM2) library
opam¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2, 1.2.1
- Build Dependencies:
- ocaml
- Link Dependencies:
- ocaml
- Description:
- OPAM: OCaml Package Manager OPAM is a source-based package manager for OCaml. It supports multiple simultaneous compiler installations, flexible package constraints, and a Git-friendly development workflow.
opari2¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1, 2.0, 1.1.4, 1.1.2
- Description:
- OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provide you with a new initialization method that allows for multi-directory and parallel builds as well as the usage of pre-instrumented libraries. Furthermore, an efficient way of tracking parent-child relationships was added. Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0 tied tasks.
openbabel¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1
- Build Dependencies:
- zlib, cairo, pkgconfig, python, eigen, cmake, libxml2
- Link Dependencies:
- python, eigen, zlib, cairo, libxml2
- Run Dependencies:
- python
- Description:
- Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
openblas¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.2.20, 0.2.19, 0.2.18, 0.2.17, 0.2.16, 0.2.15
- Description:
- OpenBLAS: An optimized BLAS library
opencoarrays¶
- Homepage:
- Spack package:
- Versions:
- 1.8.10, 1.8.4, 1.8.0, 1.7.4, 1.6.2
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- OpenCoarrays is an open-source software project that produces an application binary interface (ABI) supporting coarray Fortran (CAF) compilers, an application programming interface (API) that supports users of non-CAF compilers, and an associated compiler wrapper and program launcher.
opencv¶
- Homepage:
- Spack package:
- Versions:
- 3.3.0, 3.2.0, 3.1.0, 2.4.13.2, 2.4.13.1, 2.4.13, 2.4.12.3, 2.4.12.2, 2.4.12.1, master
- Build Dependencies:
- libpng, py-numpy, zlib, protobuf, qt, cmake, jpeg, cuda, gtkplus, java, eigen, libtiff, python, jasper, vtk
- Link Dependencies:
- libpng, zlib, protobuf, jasper, jpeg, cuda, gtkplus, java, libtiff, python, qt, vtk
- Run Dependencies:
- py-numpy
- Description:
- OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real- time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.
openexr¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.0, 2.0.1, 1.7.0, 1.6.1, 1.5.0, 1.4.0a, 1.3.2
- Build Dependencies:
- pkgconfig, ilmbase
- Link Dependencies:
- ilmbase
- Description:
- OpenEXR Graphics Tools (high dynamic-range image file format)
openfast¶
- Homepage:
- Spack package:
- Versions:
- develop, master
- Build Dependencies:
- yaml-cpp, hdf5, zlib, mpi, lapack, blas, cmake, libxml2
- Link Dependencies:
- yaml-cpp, hdf5, zlib, mpi, lapack, blas, libxml2
- Description:
- Wind turbine simulation package from NREL
openfoam-com¶
- Homepage:
- Spack package:
- Versions:
- develop, 1712, 1706, 1612
- Build Dependencies:
- metis, zlib, flex, scotch, mpi, cmake, cgal, fftw, kahip, boost, parmgridgen, paraview, zoltan
- Link Dependencies:
- metis, fftw, zlib, boost, paraview, scotch, mpi, kahip, cgal, zoltan
- Description:
- OpenFOAM is a GPL-opensource C++ CFD-toolbox. This offering is supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004.
openfoam-org¶
- Homepage:
- Spack package:
- Versions:
- develop, 5.0, 4.1
- Build Dependencies:
- scotch, mpi, cmake, zlib, flex
- Link Dependencies:
- scotch, zlib, mpi
- Description:
- OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.
openfst¶
- Homepage:
- Spack package:
- Versions:
- 1.6.1, 1.6.0, 1.5.4, 1.5.3, 1.5.2, 1.5.1, 1.5.0, 1.4.1-patch, 1.4.1, 1.4.0
- Description:
- OpenFst is a library for constructing, combining, optimizing, and searching weighted finite-state transducers (FSTs). Weighted finite- state transducers are automata where each transition has an input label, an output label, and a weight.
opengl¶
- Homepage:
- Spack package:
- Versions:
- 3.2
- Description:
- Placeholder for external OpenGL libraries from hardware vendors
openjpeg¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0, 2.2.0, 2.1.2, 2.1.1, 2.1.0, 2.0.1, 2.0.0, 1.5.2, 1.5.1
- Build Dependencies:
- cmake
- Description:
- OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since April 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.
openmc¶
- Homepage:
- Spack package:
- Versions:
- develop
- Description:
- The OpenMC project aims to provide a fully-featured Monte Carlo particle transport code based on modern methods. It is a constructive solid geometry, continuous-energy transport code that uses ACE format cross sections. The project started under the Computational Reactor Physics Group at MIT.
openmpi¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0, 2.1.2, 2.1.1, 2.1.0, 2.0.4, 2.0.3, 2.0.2, 2.0.1, 2.0.0, 1.10.7, 1.10.6, 1.10.5, 1.10.4, 1.10.3, 1.10.2, 1.10.1, 1.10.0, 1.8.8, 1.8.7, 1.8.6, 1.8.5, 1.8.4, 1.8.3, 1.8.2, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.7.3, 1.7.2, 1.7.1, 1.7, 1.6.5, 1.6.4, 1.6.3, 1.6.2, 1.6.1, 1.6, 1.5.5, 1.5.4, 1.5.3, 1.5.2, 1.5.1, 1.5, 1.4.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4, 1.3.4, 1.3.3, 1.3.2, 1.3.1, 1.3, 1.2.9, 1.2.8, 1.2.7, 1.2.6, 1.2.5, 1.2.4, 1.2.3, 1.2.2, 1.2.1, 1.2, 1.1.5, 1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1, 1.0.2, 1.0.1, 1.0
- Build Dependencies:
- hwloc, ucx, java, sqlite
- Link Dependencies:
- hwloc, ucx, java, sqlite
- Description:
- The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
opennurbs¶
- Homepage:
- Spack package:
- Versions:
- develop, percept
- Description:
- OpenNURBS is an open-source NURBS-based geometric modeling library and toolset, with meshing and display / output functions.
openscenegraph¶
- Homepage:
- Spack package:
- Versions:
- 3.2.3, 3.1.5
- Build Dependencies:
- cmake, qt, zlib
- Link Dependencies:
- qt, zlib
- Description:
- OpenSceneGraph is an open source, high performance 3D graphics toolkit that's used in a variety of visual simulation applications.
openspeedshop¶
- Homepage:
- Spack package:
- Versions:
- 2.3
- Build Dependencies:
- libmonitor, mpich2, libtool, flex, mpt, openmpi, qt, bison, mvapich2, libxml2, mvapich, boost, cbtf-argonavis, mrnet, cbtf, libunwind, dyninst, binutils, cmake, cbtf-krell, libdwarf, sqlite, papi, mpich
- Link Dependencies:
- libmonitor, mpich2, libunwind, sqlite, papi, mpt, mpich, qt, cbtf-krell, openmpi, mvapich2, elf, mrnet, mvapich, boost, cbtf-argonavis, libxml2, dyninst, cbtf, libdwarf
- Description:
- OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEs NNSA. It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet from UW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linux performance tool which is targeted to support performance analysis of applications running on both single node and large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Power8, Intel Phi, Blue Gene and Cray platforms. OpenSpeedShop development is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop are released as open source code primarily under LGPL.
openssh¶
- Homepage:
- Spack package:
- Versions:
- 7.6p1, 7.5p1, 7.4p1, 7.3p1, 7.2p2, 7.1p2, 7.0p1, 6.9p1, 6.8p1, 6.7p1, 6.6p1
- Build Dependencies:
- libedit, ncurses, openssl, zlib
- Link Dependencies:
- libedit, ncurses, openssl, zlib
- Description:
- OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options.
openssl¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0g, 1.1.0e, 1.1.0d, 1.1.0c, 1.0.2n, 1.0.2m, 1.0.2k, 1.0.2j, 1.0.2i, 1.0.2h, 1.0.2g, 1.0.2f, 1.0.2e, 1.0.2d, 1.0.1u, 1.0.1t, 1.0.1r, 1.0.1h
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- OpenSSL is an open source project that provides a robust, commercial- grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.
opium¶
- Homepage:
- Spack package:
- Versions:
- 3.8
- Build Dependencies:
- lapack, blas
- Link Dependencies:
- lapack, blas
- Description:
- DFT pseudopotential generation project
opus¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1, 1.0.3, 1.0.2, 1.0.1, 1.0.0, 0.9.14, 0.9.10, 0.9.9, 0.9.8, 0.9.7, 0.9.6, 0.9.5, 0.9.3, 0.9.2, 0.9.1, 0.9.0
- Build Dependencies:
- libvorbis
- Link Dependencies:
- libvorbis
- Description:
- Opus is a totally open, royalty-free, highly versatile audio codec.
orfm¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1
- Description:
- A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences.
orthomcl¶
- Homepage:
- Spack package:
- Versions:
- 2.0.9
- Build Dependencies:
- perl, mcl, mariadb, blast-plus
- Link Dependencies:
- mcl, mariadb, blast-plus
- Run Dependencies:
- perl
- Description:
- OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.
osu-micro-benchmarks¶
- Homepage:
- Spack package:
- Versions:
- 5.4, 5.3
- Build Dependencies:
- cuda, mpi
- Link Dependencies:
- cuda, mpi
- Description:
- The Ohio MicroBenchmark suite is a collection of independent MPI message passing performance microbenchmarks developed and written at The Ohio State University. It includes traditional benchmarks and performance measures such as latency, bandwidth and host overhead and can be used for both traditional and GPU-enhanced nodes.
otf¶
- Homepage:
- Spack package:
- Versions:
- 1.12.5salmon
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- To improve scalability for very large and massively parallel traces the Open Trace Format (OTF) is developed at ZIH as a successor format to the Vampir Trace Format (VTF3).
otf2¶
- Homepage:
- Spack package:
- Versions:
- 2.1, 2.0, 1.5.1, 1.4, 1.3.1, 1.2.1
- Description:
- The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library.
p4est¶
- Homepage:
- Spack package:
- Versions:
- 2.0, 1.1
- Build Dependencies:
- automake, autoconf, zlib, libtool, mpi
- Link Dependencies:
- zlib, mpi
- Description:
- Dynamic management of a collection (a forest) of adaptive octrees in parallel
pacbio-daligner¶
- Homepage:
- Spack package:
- Versions:
- 2017-08-05
- Build Dependencies:
- pacbio-dazz-db, gmake
- Link Dependencies:
- pacbio-dazz-db
- Description:
- Daligner: The Dazzler "Overlap" Module. This is a special fork required for some pacbio utilities.
pacbio-damasker¶
- Homepage:
- Spack package:
- Versions:
- 2017-02-11
- Build Dependencies:
- gmake
- Description:
- Damasker: The Dazzler Repeat Masking Suite. This is a special fork required for some pacbio utilities.
pacbio-dazz-db¶
- Homepage:
- Spack package:
- Versions:
- 2017-04-10
- Build Dependencies:
- gmake
- Description:
- The Dazzler Database Library. This version is a special fork required for some pacbio utilities.
pacbio-dextractor¶
- Homepage:
- Spack package:
- Versions:
- 2016-08-09
- Build Dependencies:
- hdf5, gmake
- Link Dependencies:
- hdf5
- Description:
- The Dextractor and Compression Command Library. This is a special fork required by some pacbio utilities.
pagit¶
- Homepage:
- Spack package:
- Versions:
- 1.01
- Build Dependencies:
- perl, java
- Run Dependencies:
- perl, java
- Description:
- PAGIT addresses the need for software to generate high quality draft genomes.
pagmo¶
- Homepage:
- Spack package:
- Versions:
- 1.1.7
- Build Dependencies:
- python, boost, py-scipy, mpi, ipopt, py-networkx, cmake, gsl, blas
- Link Dependencies:
- boost, mpi, ipopt, gsl, python, blas
- Run Dependencies:
- py-scipy, py-networkx
- Description:
- Parallel Global Multiobjective Optimizer (and its Python alter ego PyGMO) is a C++ / Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.
paml¶
- Homepage:
- Spack package:
- Versions:
- 4.9e
- Description:
- PAML is a package of programs for phylogenetic analyses of DNA or protein sewuences using maximum likelihood.
panda¶
- Homepage:
- Spack package:
- Versions:
- 2016-03-07
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- PANDA: Parallel AdjaceNcy Decomposition Algorithm
pandaseq¶
- Homepage:
- Spack package:
- Versions:
- 2.11, 2.10
- Build Dependencies:
- pkg-config, autoconf, m4, zlib, libtool, automake
- Description:
- PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
pango¶
- Homepage:
- Spack package:
- Versions:
- 1.41.0, 1.40.3, 1.40.1, 1.36.8
- Build Dependencies:
- cairo, pkgconfig, harfbuzz, gobject-introspection, glib, libxft
- Link Dependencies:
- harfbuzz, gobject-introspection, cairo, libxft, glib
- Description:
- Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit.
papi¶
- Homepage:
- Spack package:
- Versions:
- 5.5.1, 5.5.0, 5.4.3, 5.4.1, 5.3.0
- Description:
- PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
paradiseo¶
- Homepage:
- Spack package:
- Versions:
- head, dev-safe
- Build Dependencies:
- gnuplot, doxygen, boost, mpi, eigen, cmake
- Link Dependencies:
- gnuplot, boost, mpi
- Description:
- A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.
parallel¶
- Homepage:
- Spack package:
- Versions:
- 20170322, 20170122, 20160422, 20160322
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input.
parallel-netcdf¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0, 1.7.0, 1.6.1
- Build Dependencies:
- m4, mpi
- Link Dependencies:
- mpi
- Description:
- Parallel netCDF (PnetCDF) is a library providing high-performance parallel I/O while still maintaining file-format compatibility with Unidata's NetCDF.
paraver¶
- Homepage:
- Spack package:
- Versions:
- 4.6.3, 4.6.2
- Build Dependencies:
- wx, boost, wxpropgrid
- Link Dependencies:
- wx, boost, wxpropgrid
- Description:
- "A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.
paraview¶
- Homepage:
- Spack package:
- Versions:
- 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
- Build Dependencies:
- libpng, hdf5, zlib, libxt, qt, mpi, cmake, mesa, jpeg, freetype, bzip2, libtiff, python, libxml2
- Link Dependencies:
- libpng, hdf5, zlib, libxt, qt, mpi, mesa, jpeg, freetype, bzip2, libtiff, python, libxml2
- Run Dependencies:
- py-numpy, py-matplotlib
- Description:
- ParaView is an open-source, multi-platform data analysis and visualization application.
parmetis¶
- Homepage:
- Spack package:
- Versions:
- 4.0.3, 4.0.2
- Build Dependencies:
- metis, cmake, mpi
- Link Dependencies:
- metis, mpi
- Description:
- ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
parmgridgen¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- MGRIDGEN is a serial library written entirely in ANSI C that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParMGridGen is the parallel version of MGridGen.
parsimonator¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Description:
- Parsimonator is a no-frills light-weight implementation for building starting trees under parsimony for RAxML
parsplice¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1
- Build Dependencies:
- nauty, berkeley-db, boost, mpi, lammps, eigen, cmake
- Link Dependencies:
- nauty, berkeley-db, boost, mpi, lammps, eigen
- Description:
- ParSplice code implements the Parallel Trajectory Splicing algorithm
partitionfinder¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1
- Build Dependencies:
- py-numpy, py-scikit-learn, py-pytables, py-scipy, python, py-pandas, py-pyparsing
- Run Dependencies:
- py-numpy, py-scikit-learn, py-pytables, py-scipy, python, py-pandas, py-pyparsing
- Description:
- PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.
patch¶
- Homepage:
- Spack package:
- Versions:
- 2.7.5
- Description:
- Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions.
patchelf¶
- Homepage:
- Spack package:
- Versions:
- 0.9, 0.8
- Description:
- PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
pathfinder¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Description:
- Proxy Application. Signature search.
pax-utils¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Description:
- ELF utils that can check files for security relevant properties
pbmpi¶
- Homepage:
- Spack package:
- Versions:
- partition
- Build Dependencies:
- libfabric, mpi
- Link Dependencies:
- libfabric, mpi
- Description:
- A Bayesian software for phylogenetic reconstruction using mixture models
pcma¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Description:
- PCMA is a progressive multiple sequence alignment program that combines two different alignment strategies.
pcre¶
- Homepage:
- Spack package:
- Versions:
- 8.41, 8.40, 8.39, 8.38
- Description:
- The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.
pcre2¶
- Homepage:
- Spack package:
- Versions:
- 10.20
- Description:
- The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.
pdsh¶
- Homepage:
- Spack package:
- Versions:
- 2.31
- Description:
- PDSH: a high performance, parallel remote shell utility
pdt¶
- Homepage:
- Spack package:
- Versions:
- 3.22.1, 3.22, 3.21, 3.20, 3.19, 3.18.1
- Description:
- Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
pegtl¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1.4, 2.0.0
- Build Dependencies:
- cmake
- Description:
- The Parsing Expression Grammar Template Library (PEGTL) is a zero- dependency C++11 header-only library for creating parsers according to a Parsing Expression Grammar (PEG).
pennant¶
- Homepage:
- Spack package:
- Versions:
- 0.9, 0.8, 0.7, 0.6, 0.5, 0.4
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- PENNANT is an unstructured mesh physics mini-app designed for advanced architecture research. It contains mesh data structures and a few physics algorithms adapted from the LANL rad-hydro code FLAG, and gives a sample of the typical memory access patterns of FLAG.
percept¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- yaml-cpp, trilinos, boost, cmake, googletest, opennurbs
- Link Dependencies:
- opennurbs, yaml-cpp, trilinos, boost, googletest
- Description:
- Parallel mesh refinement and adaptivity tools for the finite element method.
perl¶
- Homepage:
- Spack package:
- Versions:
- 5.25.11, 5.24.1, 5.22.3, 5.22.2, 5.22.1, 5.22.0, 5.20.3, 5.18.4, 5.16.3
- Build Dependencies:
- gdbm
- Link Dependencies:
- gdbm
- Description:
- Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.
perl-algorithm-diff¶
- Homepage:
- Spack package:
- Versions:
- 1.1903
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Compute 'intelligent' differences between two files / lists
perl-app-cmd¶
- Homepage:
- Spack package:
- Versions:
- 0.331
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Write command line apps with less suffering
perl-array-utils¶
- Homepage:
- Spack package:
- Versions:
- 0.5
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Small utils for array manipulation
perl-b-hooks-endofscope¶
- Homepage:
- Spack package:
- Versions:
- 0.21
- Build Dependencies:
- perl, perl-sub-exporter-progressive
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-sub-exporter-progressive
- Description:
- Execute code after a scope finished compilation.
perl-bio-perl¶
- Homepage:
- Spack package:
- Versions:
- 1.007002
- Build Dependencies:
- perl, perl-io-string, perl-test-most, perl-data-stag, perl-module-build, perl-uri-escape
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-uri-escape, perl-io-string, perl-data-stag, perl-test-most
- Description:
- Functional access to BioPerl for people who don't know objects
perl-bit-vector¶
- Homepage:
- Spack package:
- Versions:
- 7.4
- Build Dependencies:
- perl, perl-carp-clan
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-carp-clan
- Description:
- Efficient bit vector, set of integers and "big int" math library
perl-capture-tiny¶
- Homepage:
- Spack package:
- Versions:
- 0.46
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Capture STDOUT and STDERR from Perl, XS or external programs
perl-carp-clan¶
- Homepage:
- Spack package:
- Versions:
- 6.06
- Build Dependencies:
- perl, perl-sub-uplevel, perl-test-exception
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-sub-uplevel, perl-test-exception
- Description:
- Report errors from perspective of caller of a "clan" of modules
perl-class-data-inheritable¶
- Homepage:
- Spack package:
- Versions:
- 0.08
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- For creating accessor/mutators to class data.
perl-class-inspector¶
- Homepage:
- Spack package:
- Versions:
- 1.32
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Get information about a class and its structure
perl-class-load¶
- Homepage:
- Spack package:
- Versions:
- 0.24
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- A working (require "Class::Name") and more
perl-class-load-xs¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- perl, perl-class-load
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-class-load
- Description:
- This module provides an XS implementation for portions of Class::Load.
perl-cpan-meta-check¶
- Homepage:
- Spack package:
- Versions:
- 0.014
- Build Dependencies:
- perl-test-deep, perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl-test-deep, perl
- Description:
- This module verifies if requirements described in a CPAN::Meta object are present..
perl-data-optlist¶
- Homepage:
- Spack package:
- Versions:
- 0.110
- Build Dependencies:
- perl, perl-sub-install
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-sub-install
- Description:
- Parse and validate simple name/value option pairs
perl-data-stag¶
- Homepage:
- Spack package:
- Versions:
- 0.14
- Build Dependencies:
- perl, perl-io-string
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-io-string
- Description:
- Structured Tags datastructures
perl-dbd-mysql¶
- Homepage:
- Spack package:
- Versions:
- 4.043
- Build Dependencies:
- perl-test-deep, perl, mariadb, perl-dbi
- Link Dependencies:
- perl, mariadb
- Run Dependencies:
- perl-test-deep, perl, perl-dbi
- Description:
- MySQL driver for the Perl5 Database Interface (DBI)
perl-dbfile¶
- Homepage:
- Spack package:
- Versions:
- 1.840
- Build Dependencies:
- perl, perl-extutils-makemaker
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see "Using DB_File with Berkeley DB version 2 or greater"). It is assumed that you have a copy of the Berkeley DB manual pages at hand when reading this documentation. The interface defined here mirrors the Berkeley DB interface closely.
perl-dbi¶
- Homepage:
- Spack package:
- Versions:
- 1.636
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- The DBI is the standard database interface module for Perl. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used.
perl-devel-cycle¶
- Homepage:
- Spack package:
- Versions:
- 1.12
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Find memory cycles in objects
perl-devel-globaldestruction¶
- Homepage:
- Spack package:
- Versions:
- 0.14
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Makes Perl's global destruction less tricky to deal with
perl-devel-overloadinfo¶
- Homepage:
- Spack package:
- Versions:
- 0.004
- Build Dependencies:
- perl, perl-mro-compat
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-mro-compat
- Description:
- Returns information about overloaded operators for a given class
perl-devel-stacktrace¶
- Homepage:
- Spack package:
- Versions:
- 2.02
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- An object representing a stack trace.
perl-digest-md5¶
- Homepage:
- Spack package:
- Versions:
- 2.55
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl interface to the MD5 Algorithm
perl-dist-checkconflicts¶
- Homepage:
- Spack package:
- Versions:
- 0.11
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Declare version conflicts for your dist
perl-encode-locale¶
- Homepage:
- Spack package:
- Versions:
- 1.05
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Determine the locale encoding
perl-eval-closure¶
- Homepage:
- Spack package:
- Versions:
- 0.14
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Safely and cleanly create closures via string eval
perl-exception-class¶
- Homepage:
- Spack package:
- Versions:
- 1.43
- Build Dependencies:
- perl, perl-devel-stacktrace, perl-class-data-inheritable
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-devel-stacktrace, perl-class-data-inheritable
- Description:
- A module that allows you to declare real exception classes in Perl
perl-exporter-tiny¶
- Homepage:
- Spack package:
- Versions:
- 1.000000
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- An exporter with the features of Sub::Exporter but only core dependencies
perl-extutils-makemaker¶
- Homepage:
- Spack package:
- Versions:
- 7.24
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- ExtUtils::MakeMaker - Create a module Makefile. This utility is designed to write a Makefile for an extension module from a Makefile.PL. It is based on the Makefile.SH model provided by Andy Dougherty and the perl5-porters.
perl-extutils-pkgconfig¶
- Homepage:
- Spack package:
- Versions:
- 1.16
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- simplistic interface to pkg-config
perl-file-copy-recursive¶
- Homepage:
- Spack package:
- Versions:
- 0.38
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl extension for recursively copying files and directories
perl-file-listing¶
- Homepage:
- Spack package:
- Versions:
- 6.04
- Build Dependencies:
- perl, perl-http-date
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-http-date
- Description:
- Parse directory listing
perl-file-pushd¶
- Homepage:
- Spack package:
- Versions:
- 1.014
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Change directory temporarily for a limited scope
perl-file-slurp-tiny¶
- Homepage:
- Spack package:
- Versions:
- 0.004
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- A simple, sane and efficient file slurper
perl-file-which¶
- Homepage:
- Spack package:
- Versions:
- 1.22
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl implementation of the which utility as an API
perl-font-ttf¶
- Homepage:
- Spack package:
- Versions:
- 1.06
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl module for TrueType Font hacking
perl-gd¶
- Homepage:
- Spack package:
- Versions:
- 2.53
- Build Dependencies:
- perl-extutils-pkgconfig, perl, libgd, perl-module-build, perl-extutils-makemaker
- Link Dependencies:
- perl, libgd
- Run Dependencies:
- perl-extutils-pkgconfig, perl, perl-extutils-makemaker
- Description:
- Interface to Gd Graphics Library
perl-gd-graph¶
- Homepage:
- Spack package:
- Versions:
- 1.4308
- Build Dependencies:
- perl, perl-capture-tiny, perl-gd-text, perl-gd, perl-test-exception
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-capture-tiny, perl-gd-text, perl-gd, perl-test-exception
- Description:
- Graph Plotting Module for Perl 5
perl-gd-text¶
- Homepage:
- Spack package:
- Versions:
- 0.86
- Build Dependencies:
- perl, perl-gd
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-gd
- Description:
- Text utilities for use with GD
perl-graph¶
- Homepage:
- Spack package:
- Versions:
- 0.9704
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Graph data structures and algorithms
perl-html-parser¶
- Homepage:
- Spack package:
- Versions:
- 3.72
- Build Dependencies:
- perl, perl-html-tagset
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-html-tagset
- Description:
- HTML parser class
perl-html-tagset¶
- Homepage:
- Spack package:
- Versions:
- 3.20
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Data tables useful in parsing HTML
perl-http-cookies¶
- Homepage:
- Spack package:
- Versions:
- 6.04
- Build Dependencies:
- perl, perl-http-message, perl-uri
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-http-message, perl-uri
- Description:
- HTTP cookie jars
perl-http-daemon¶
- Homepage:
- Spack package:
- Versions:
- 6.01
- Build Dependencies:
- perl, perl-http-message, perl-lwp-mediatypes
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-http-message, perl-lwp-mediatypes
- Description:
- A simple http server class
perl-http-date¶
- Homepage:
- Spack package:
- Versions:
- 6.02
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Date conversion routines
perl-http-message¶
- Homepage:
- Spack package:
- Versions:
- 6.13
- Build Dependencies:
- perl, perl-io-html, perl-lwp-mediatypes, perl-try-tiny, perl-uri, perl-http-date, perl-encode-locale
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-io-html, perl-lwp-mediatypes, perl-try-tiny, perl-uri, perl-http-date, perl-encode-locale
- Description:
- HTTP style message (base class)
perl-http-negotiate¶
- Homepage:
- Spack package:
- Versions:
- 6.01
- Build Dependencies:
- perl, perl-http-message
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-http-message
- Description:
- Choose a variant to serve
perl-inline¶
- Homepage:
- Spack package:
- Versions:
- 0.80
- Build Dependencies:
- perl, perl-test-warn
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-test-warn
- Description:
- Write Perl Subroutines in Other Programming Languages
perl-inline-c¶
- Homepage:
- Spack package:
- Versions:
- 0.78
- Build Dependencies:
- perl-file-copy-recursive, perl-pegex, perl-inline, perl, perl-yaml-libyaml, perl-parse-recdescent
- Link Dependencies:
- perl
- Run Dependencies:
- perl-file-copy-recursive, perl-pegex, perl-inline, perl, perl-yaml-libyaml, perl-parse-recdescent
- Description:
- C Language Support for Inline
perl-intervaltree¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- perl, perl-extutils-makemaker
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup.
perl-io-html¶
- Homepage:
- Spack package:
- Versions:
- 1.001
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Open an HTML file with automatic charset detection.
perl-io-sessiondata¶
- Homepage:
- Spack package:
- Versions:
- 1.03
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- A wrapper around a single IO::Socket object
perl-io-socket-ssl¶
- Homepage:
- Spack package:
- Versions:
- 2.052
- Build Dependencies:
- perl, perl-net-ssleay
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-net-ssleay
- Description:
- SSL sockets with IO::Socket interface
perl-io-string¶
- Homepage:
- Spack package:
- Versions:
- 1.08
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Emulate file interface for in-core strings
perl-list-moreutils¶
- Homepage:
- Spack package:
- Versions:
- 0.428
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Provide the stuff missing in List::Util
perl-log-log4perl¶
- Homepage:
- Spack package:
- Versions:
- 146
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Log4j implementation for Perl
perl-lwp¶
- Homepage:
- Spack package:
- Versions:
- 6.29
- Build Dependencies:
- perl, perl-http-cookies, perl-http-message, perl-test-requiresinternet, perl-http-negotiate, perl-html-parser, perl-http-daemon, perl-www-robotrules, perl-file-listing, perl-test-fatal, perl-net-http
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-http-cookies, perl-http-message, perl-test-requiresinternet, perl-http-negotiate, perl-html-parser, perl-http-daemon, perl-www-robotrules, perl-file-listing, perl-test-fatal, perl-net-http
- Description:
- The World-Wide Web library for Perl
perl-lwp-mediatypes¶
- Homepage:
- Spack package:
- Versions:
- 6.02
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Guess media type for a file or a URL
perl-lwp-protocol-https¶
- Homepage:
- Spack package:
- Versions:
- 6.04
- Build Dependencies:
- perl, perl-io-socket-ssl, perl-lwp, perl-test-requiresinternet, perl-mozilla-ca, perl-net-http
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-io-socket-ssl, perl-lwp, perl-test-requiresinternet, perl-mozilla-ca, perl-net-http
- Description:
- Provide https support for LWP::UserAgent
perl-math-cdf¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Generate probabilities and quantiles from several statistical probability functions
perl-module-build¶
- Homepage:
- Spack package:
- Versions:
- 0.4220
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Module::Build is a system for building, testing, and installing Perl modules. It is meant to be an alternative to ExtUtils::MakeMaker. Developers may alter the behavior of the module through subclassing in a much more straightforward way than with MakeMaker. It also does not require a make on your system - most of the Module::Build code is pure- perl and written in a very cross-platform way.
perl-module-runtime-conflicts¶
- Homepage:
- Spack package:
- Versions:
- 0.003
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Provide information on conflicts for Module::Runtime
perl-moose¶
- Homepage:
- Spack package:
- Versions:
- 2.2006
- Build Dependencies:
- perl-sub-name, perl-devel-globaldestruction, perl-package-stash-xs, perl, perl-test-cleannamespaces, perl-devel-overloadinfo, perl-class-load-xs, perl-package-deprecationmanager, perl-devel-stacktrace, perl-eval-closure, perl-cpan-meta-check, perl-module-runtime-conflicts
- Link Dependencies:
- perl
- Run Dependencies:
- perl-sub-name, perl-devel-globaldestruction, perl-package-stash-xs, perl, perl-test-cleannamespaces, perl-devel-overloadinfo, perl-class-load-xs, perl-package-deprecationmanager, perl-devel-stacktrace, perl-eval-closure, perl-cpan-meta-check, perl-module-runtime-conflicts
- Description:
- A postmodern object system for Perl 5
perl-mozilla-ca¶
- Homepage:
- Spack package:
- Versions:
- 20160104
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Mozilla's CA cert bundle in PEM format
perl-mro-compat¶
- Homepage:
- Spack package:
- Versions:
- 0.13
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Provides several utilities for dealing with method resolution order.
perl-namespace-clean¶
- Homepage:
- Spack package:
- Versions:
- 0.27
- Build Dependencies:
- perl, perl-b-hooks-endofscope
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-b-hooks-endofscope
- Description:
- Keep imports and functions out of your namespace.
perl-net-http¶
- Homepage:
- Spack package:
- Versions:
- 6.17
- Build Dependencies:
- perl, perl-uri
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-uri
- Description:
- Low-level HTTP connection (client)
perl-net-ssleay¶
- Homepage:
- Spack package:
- Versions:
- 1.82
- Build Dependencies:
- perl, openssl
- Link Dependencies:
- perl, openssl
- Run Dependencies:
- perl
- Description:
- Perl extension for using OpenSSL
perl-package-deprecationmanager¶
- Homepage:
- Spack package:
- Versions:
- 0.17
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Manage deprecation warnings for your distribution
perl-package-stash¶
- Homepage:
- Spack package:
- Versions:
- 0.37
- Build Dependencies:
- perl, perl-test-fatal, perl-test-requires, perl-module-implementation, perl-dist-checkconflicts
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-test-fatal, perl-test-requires, perl-module-implementation, perl-dist-checkconflicts
- Description:
- Routines for manipulating stashes
perl-package-stash-xs¶
- Homepage:
- Spack package:
- Versions:
- 0.28
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Faster and more correct implementation of the Package::Stash API
perl-padwalker¶
- Homepage:
- Spack package:
- Versions:
- 2.2
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- play with other peoples' lexical variables
perl-params-util¶
- Homepage:
- Spack package:
- Versions:
- 1.07
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Simple, compact and correct param-checking functions
perl-parse-recdescent¶
- Homepage:
- Spack package:
- Versions:
- 1.967015
- Build Dependencies:
- perl, perl-module-build
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Generate Recursive-Descent Parsers
perl-pdf-api2¶
- Homepage:
- Spack package:
- Versions:
- 2.033
- Build Dependencies:
- perl, perl-test-memory-cycle, perl-font-ttf, perl-test-exception
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-test-memory-cycle, perl-font-ttf, perl-test-exception
- Description:
- Facilitates the creation and modification of PDF files
perl-pegex¶
- Homepage:
- Spack package:
- Versions:
- 0.64
- Build Dependencies:
- perl, perl-file-sharedir-install, perl-yaml-libyaml
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-file-sharedir-install, perl-yaml-libyaml
- Description:
- Acmeist PEG Parser Framework
perl-perlio-gzip¶
- Homepage:
- Spack package:
- Versions:
- 0.20, 0.19
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl extension to provide a PerlIO layer to gzip/gunzip
perl-soap-lite¶
- Homepage:
- Spack package:
- Versions:
- 1.22
- Build Dependencies:
- perl, perl-xml-parser, perl-lwp-protocol-https, perl-task-weaken, perl-xml-parser-lite, perl-io-sessiondata, perl-class-inspector, perl-test-warn
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-xml-parser, perl-lwp-protocol-https, perl-task-weaken, perl-xml-parser-lite, perl-io-sessiondata, perl-class-inspector, perl-test-warn
- Description:
- Perl's Web Services Toolkit
perl-star-fusion¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- perl, perl-intervaltree, star, perl-dbi, perl-dbfile, perl-uri-escape
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-intervaltree, star, perl-dbi, perl-dbfile, perl-uri-escape
- Description:
- STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
perl-statistics-descriptive¶
- Homepage:
- Spack package:
- Versions:
- 3.0612
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Module of basic descriptive statistical functions.
perl-sub-exporter¶
- Homepage:
- Spack package:
- Versions:
- 0.987
- Build Dependencies:
- perl-params-util, perl, perl-data-optlist
- Link Dependencies:
- perl
- Run Dependencies:
- perl-params-util, perl, perl-data-optlist
- Description:
- A sophisticated exporter for custom-built routines
perl-sub-exporter-progressive¶
- Homepage:
- Spack package:
- Versions:
- 0.001013
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Progressive Sub::Exporter
perl-sub-identify¶
- Homepage:
- Spack package:
- Versions:
- 0.14
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Retrieve names of code references
perl-sub-install¶
- Homepage:
- Spack package:
- Versions:
- 0.928
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Install subroutines into packages easily
perl-sub-name¶
- Homepage:
- Spack package:
- Versions:
- 0.21
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Name or rename a sub
perl-sub-uplevel¶
- Homepage:
- Spack package:
- Versions:
- 0.2800
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- apparently run a function in a higher stack frame
perl-svg¶
- Homepage:
- Spack package:
- Versions:
- 2.78
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl extension for generating Scalable Vector Graphics (SVG) documents.
perl-swissknife¶
- Homepage:
- Spack package:
- Versions:
- 1.75
- Build Dependencies:
- perl, perl-module-build
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- An object-oriented Perl library to handle Swiss-Prot entries
perl-task-weaken¶
- Homepage:
- Spack package:
- Versions:
- 1.04
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Ensure that a platform has weaken support
perl-term-readkey¶
- Homepage:
- Spack package:
- Versions:
- 2.37
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized handy functions for working with terminals. One of the main goals is to have the functions as portable as possible, so you can just plug in "use Term::ReadKey" on any architecture and have a good likelihood of it working.
perl-test-cleannamespaces¶
- Homepage:
- Spack package:
- Versions:
- 0.22
- Build Dependencies:
- perl-test-needs, perl, perl-module-runtime, perl-sub-exporter, perl-namespace-clean, perl-test-deep, perl-sub-identify, perl-file-pushd, perl-package-stash, perl-test-warnings
- Link Dependencies:
- perl
- Run Dependencies:
- perl-test-needs, perl, perl-module-runtime, perl-sub-exporter, perl-namespace-clean, perl-test-deep, perl-sub-identify, perl-file-pushd, perl-package-stash, perl-test-warnings
- Description:
- This module lets you check your module's namespaces for imported functions you might have forgotten to remove
perl-test-deep¶
- Homepage:
- Spack package:
- Versions:
- 1.127
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Extremely flexible deep comparison
perl-test-differences¶
- Homepage:
- Spack package:
- Versions:
- 0.64
- Build Dependencies:
- perl, perl-capture-tiny, perl-module-build, perl-text-diff
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-capture-tiny, perl-text-diff
- Description:
- Test strings and data structures and show differences if not ok
perl-test-exception¶
- Homepage:
- Spack package:
- Versions:
- 0.43
- Build Dependencies:
- perl, perl-sub-uplevel
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-sub-uplevel
- Description:
- Test exception-based code
perl-test-fatal¶
- Homepage:
- Spack package:
- Versions:
- 0.014
- Build Dependencies:
- perl, perl-try-tiny
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-try-tiny
- Description:
- Incredibly simple helpers for testing code with exceptions
perl-test-memory-cycle¶
- Homepage:
- Spack package:
- Versions:
- 1.06
- Build Dependencies:
- perl, perl-devel-cycle, perl-padwalker
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-devel-cycle, perl-padwalker
- Description:
- Check for memory leaks and circular memory references
perl-test-most¶
- Homepage:
- Spack package:
- Versions:
- 0.35
- Build Dependencies:
- perl-test-differences, perl, perl-exception-class, perl-test-deep, perl-test-exception, perl-test-warn
- Link Dependencies:
- perl
- Run Dependencies:
- perl-test-differences, perl, perl-exception-class, perl-test-deep, perl-test-exception, perl-test-warn
- Description:
- Most commonly needed test functions and features.
perl-test-needs¶
- Homepage:
- Spack package:
- Versions:
- 0.002005
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Skip tests when modules not available.
perl-test-requires¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Checks to see if the module can be loaded.
perl-test-requiresinternet¶
- Homepage:
- Spack package:
- Versions:
- 0.05
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Easily test network connectivity
perl-test-warn¶
- Homepage:
- Spack package:
- Versions:
- 0.30
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl extension to test methods for warnings
perl-test-warnings¶
- Homepage:
- Spack package:
- Versions:
- 0.026
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Test for warnings and the lack of them
perl-text-diff¶
- Homepage:
- Spack package:
- Versions:
- 1.45
- Build Dependencies:
- perl, perl-algorithm-diff
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-algorithm-diff
- Description:
- Provides a basic set of services akin to the GNU diff utility.
perl-text-unidecode¶
- Homepage:
- Spack package:
- Versions:
- 1.30
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- plain ASCII transliterations of Unicode text
perl-time-hires¶
- Homepage:
- Spack package:
- Versions:
- 1.9746
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- High resolution alarm, sleep, gettimeofday, interval timers
perl-time-piece¶
- Homepage:
- Spack package:
- Versions:
- 1.3203
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Object Oriented time objects
perl-try-tiny¶
- Homepage:
- Spack package:
- Versions:
- 0.28
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Minimal try/catch with proper preservation of $@
perl-uri¶
- Homepage:
- Spack package:
- Versions:
- 1.72
- Build Dependencies:
- perl-test-needs, perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl-test-needs, perl
- Description:
- Uniform Resource Identifiers (absolute and relative)
perl-uri-escape¶
- Homepage:
- Spack package:
- Versions:
- 1.71
- Build Dependencies:
- perl, perl-extutils-makemaker
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- This module provides functions to percent-encode and percent-decode URI strings as defined by RFC 3986. Percent-encoding URI's is informally called "URI escaping". This is the terminology used by this module, which predates the formalization of the terms by the RFC by several years.
perl-version¶
- Homepage:
- Spack package:
- Versions:
- 1.013_03
- Build Dependencies:
- perl, perl-file-slurp-tiny
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-file-slurp-tiny
- Description:
- Parse and manipulate Perl version strings
perl-www-robotrules¶
- Homepage:
- Spack package:
- Versions:
- 6.02
- Build Dependencies:
- perl, perl-uri
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-uri
- Description:
- Database of robots.txt-derived permissions
perl-xml-libxml¶
- Homepage:
- Spack package:
- Versions:
- 2.0132
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- This module is an interface to libxml2, providing XML and HTML parsers with DOM, SAX and XMLReader interfaces
perl-xml-parser¶
- Homepage:
- Spack package:
- Versions:
- 2.44
- Build Dependencies:
- perl, expat
- Link Dependencies:
- perl, expat
- Run Dependencies:
- perl
- Description:
- XML::Parser - A perl module for parsing XML documents
perl-xml-parser-lite¶
- Homepage:
- Spack package:
- Versions:
- 0.721
- Build Dependencies:
- perl, perl-test-requires
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-test-requires
- Description:
- Lightweight pure-perl XML Parser (based on regexps)
perl-xml-simple¶
- Homepage:
- Spack package:
- Versions:
- 2.24
- Build Dependencies:
- perl, perl-xml-parser
- Link Dependencies:
- perl
- Run Dependencies:
- perl, perl-xml-parser
- Description:
- An API for simple XML files
perl-yaml-libyaml¶
- Homepage:
- Spack package:
- Versions:
- 0.67
- Build Dependencies:
- perl
- Link Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl YAML Serialization using XS and libyaml
petsc¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.8.3, 3.8.2, 3.8.1, 3.8.0, 3.7.7, 3.7.6, 3.7.5, 3.7.4, 3.7.2, 3.6.4, 3.6.3, 3.5.3, 3.5.2, 3.5.1, 3.4.4, xsdk-0.2.0
- Build Dependencies:
- hypre, metis, hdf5, zlib, parmetis, lapack, scalapack, mpi, sowing, trilinos, mumps, superlu-dist, blas, python, boost
- Link Dependencies:
- hypre, metis, hdf5, zlib, parmetis, lapack, scalapack, mpi, sowing, trilinos, mumps, superlu-dist, blas, boost
- Description:
- PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
pexsi¶
- Homepage:
- Spack package:
- Versions:
- 0.10.2, 0.9.2, 0.9.0
- Build Dependencies:
- parmetis, superlu-dist
- Link Dependencies:
- parmetis, superlu-dist
- Description:
- The PEXSI library is written in C++, and uses message passing interface (MPI) to parallelize the computation on distributed memory computing systems and achieve scalability on more than 10,000 processors. The Pole EXpansion and Selected Inversion (PEXSI) method is a fast method for electronic structure calculation based on Kohn-Sham density functional theory. It efficiently evaluates certain selected elements of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian, which yields a density matrix. It can be used as an alternative to diagonalization methods for obtaining the density, energy and forces in electronic structure calculations.
pfft¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8-alpha
- Build Dependencies:
- fftw, mpi
- Link Dependencies:
- fftw, mpi
- Description:
- PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition.
pflotran¶
- Homepage:
- Spack package:
- Versions:
- develop, xsdk-0.3.0, xsdk-0.2.0
- Build Dependencies:
- hdf5, petsc, mpi
- Link Dependencies:
- hdf5, petsc, mpi
- Description:
- PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code.
pfunit¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.2.9
- Build Dependencies:
- cmake, python, mpi
- Link Dependencies:
- mpi
- Run Dependencies:
- python, py-unittest2
- Description:
- pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.
pgdspider¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1.2
- Build Dependencies:
- bcftools, java, samtools, bwa
- Link Dependencies:
- bcftools, samtools, bwa
- Run Dependencies:
- java
- Description:
- "PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs
pgi¶
- Homepage:
- Spack package:
- Versions:
- 17.10, 17.4, 17.3, 16.10, 16.5, 16.3, 15.7
- Description:
- PGI optimizing multi-core x64 compilers for Linux, MacOS & Windows with support for debugging and profiling of local MPI processes. Note: The PGI compilers are licensed software. You will need to create an account on the PGI homepage and download PGI yourself. Spack will search your current directory for the download tarball. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
phantompeakqualtools¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- awk, r-phantompeakqualtools, samtools, r
- Link Dependencies:
- awk, samtools, r
- Run Dependencies:
- r-phantompeakqualtools, r
- Description:
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.
phasta¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.0.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- SCOREC RPI's Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) of compressible and incompressible Navier Stokes equations.
phylip¶
- Homepage:
- Spack package:
- Versions:
- 3.696
- Description:
- PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
picard¶
- Homepage:
- Spack package:
- Versions:
- 2.17.0, 2.16.0, 2.15.0, 2.13.2, 2.10.0, 2.9.4, 2.9.3, 2.9.2, 2.9.0, 2.8.3, 2.6.0, 1.140
- Run Dependencies:
- java
- Description:
- Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pidx¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- PIDX Parallel I/O Library. PIDX is an efficient parallel I/O library that reads and writes multiresolution IDX data files.
pigz¶
- Homepage:
- Spack package:
- Versions:
- 2.3.4
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- A parallel implementation of gzip for modern multi-processor, multi-core machines.
piranha¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.5
- Build Dependencies:
- boost, mpfr, cmake, bzip2, python, gmp
- Link Dependencies:
- gmp, mpfr, python, boost, bzip2
- Description:
- Piranha is a computer-algebra library for the symbolic manipulation of sparse multivariate polynomials and other closely-related symbolic objects (such as Poisson series).
pixman¶
- Homepage:
- Spack package:
- Versions:
- 0.34.0, 0.32.6
- Build Dependencies:
- pkgconfig, libpng
- Link Dependencies:
- libpng
- Description:
- The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization.
pkg-config¶
- Homepage:
- Spack package:
- Versions:
- 0.29.2, 0.29.1, 0.28
- Description:
- pkg-config is a helper tool used when compiling applications and libraries
pkgconf¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0, 1.3.10, 1.3.8
- Description:
- pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility.
planck-likelihood¶
- Homepage:
- Spack package:
- Versions:
- 2.00
- Build Dependencies:
- lapack, cfitsio, blas
- Link Dependencies:
- lapack, cfitsio, blas
- Description:
- 2015 Cosmic Microwave Background (CMB) spectra and likelihood code
plasma¶
- Homepage:
- Spack package:
- Versions:
- develop, 17.1
- Build Dependencies:
- lapack, blas
- Link Dependencies:
- lapack, blas
- Description:
- Parallel Linear Algebra Software for Multicore Architectures, PLASMA is a software package for solving problems in dense linear algebra using multicore processors and Xeon Phi coprocessors. PLASMA provides implementations of state-of-the-art algorithms using cutting-edge task scheduling techniques. PLASMA currently offers a collection of routines for solving linear systems of equations, least squares problems, eigenvalue problems, and singular value problems.
plink¶
- Homepage:
- Spack package:
- Versions:
- 1.9
- Description:
- PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
plumed¶
- Homepage:
- Spack package:
- Versions:
- 2.3.3, 2.3.0, 2.2.4, 2.2.3
- Build Dependencies:
- autoconf, zlib, libtool, mpi, lapack, automake, gsl, blas
- Link Dependencies:
- lapack, gsl, blas, zlib, mpi
- Description:
- PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
pmgr-collective¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Description:
- PMGR_COLLECTIVE provides a scalable network for bootstrapping MPI jobs.
pmix¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1, 2.0.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0
- Build Dependencies:
- libevent
- Link Dependencies:
- libevent
- Description:
- The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for interprocess communication. Two versions (PMI-1 and PMI-2) have been released as part of the MPICH effort. While PMI-2 demonstrates better scaling properties than its PMI-1 predecessor, attaining rapid launch and wireup of the roughly 1M processes executing across 100k nodes expected for exascale operations remains challenging. PMI Exascale (PMIx) represents an attempt to resolve these questions by providing an extended version of the PMI definitions specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, (b) establish a standards-like body for maintaining the definitions, and (c) provide a reference implementation of the PMIx standard that demonstrates the desired level of scalability.
pnfft¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7-alpha
- Build Dependencies:
- pfft
- Link Dependencies:
- pfft
- Description:
- PNFFT is a parallel software library for the calculation of three- dimensional nonequispaced FFTs.
pngwriter¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.7.0, 0.6.0, 0.5.6, master
- Build Dependencies:
- libpng, cmake, zlib, freetype
- Link Dependencies:
- libpng, freetype, zlib
- Description:
- PNGwriter is a very easy to use open source graphics library that uses PNG as its output format. The interface has been designed to be as simple and intuitive as possible. It supports plotting and reading pixels in the RGB (red, green, blue), HSV (hue, saturation, value/brightness) and CMYK (cyan, magenta, yellow, black) colour spaces, basic shapes, scaling, bilinear interpolation, full TrueType antialiased and rotated text support, bezier curves, opening existing PNG images and more.
poamsa¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Description:
- POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.
pocl¶
- Homepage:
- Spack package:
- Versions:
- 0.14, 0.13, 0.12, 0.11, 0.10, master
- Build Dependencies:
- pkgconfig, cmake, llvm, hwloc, libtool
- Link Dependencies:
- llvm, hwloc, libtool
- Run Dependencies:
- libtool
- Description:
- Portable Computing Language (pocl) is an open source implementation of the OpenCL standard which can be easily adapted for new targets and devices, both for homogeneous CPU and heterogeneous GPUs/accelerators.
polymake¶
- Homepage:
- Spack package:
- Versions:
- 3.0r2, 3.0r1
- Build Dependencies:
- bliss, lrslib, boost, mpfr, cddlib, ppl, gmp
- Link Dependencies:
- bliss, lrslib, boost, mpfr, cddlib, ppl, gmp
- Description:
- polymake is open source software for research in polyhedral geometry
porta¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- libtool
- Description:
- PORTA is a collection of routines for analyzing polytopes and polyhedra
portage¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.1.1, 1.1.0
- Build Dependencies:
- lapack, cmake, mpi
- Link Dependencies:
- lapack, mpi
- Description:
- Portage is a framework that computational physics applications can use to build a highly customized, hybrid parallel (MPI+X) conservative remapping library for transfer of field data between meshes.
postgresql¶
- Homepage:
- Spack package:
- Versions:
- 9.5.3, 9.3.4
- Build Dependencies:
- openssl, readline
- Link Dependencies:
- openssl, readline
- Description:
- PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness.
ppl¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- gmp
- Link Dependencies:
- gmp
- Description:
- The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems. These abstractions include convex polyhedra, some special classes of polyhedra shapes that offer interesting complexity/precision tradeoffs, and grids which represent regularly spaced points that satisfy a set of linear congruence relations. The library also supports finite powersets and products of polyhedra and grids, a mixed integer linear programming problem solver using an exact-arithmetic version of the simplex algorithm, a parametric integer programming solver, and primitives for termination analysis via the automatic synthesis of linear ranking functions.
prank¶
- Homepage:
- Spack package:
- Versions:
- 150803
- Build Dependencies:
- exonerate, mafft, bpp-suite
- Link Dependencies:
- exonerate, mafft, bpp-suite
- Description:
- A powerful multiple sequence alignment browser.
presentproto¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Present protocol specification and Xlib/Xserver headers.
preseq¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2
- Build Dependencies:
- gsl, samtools
- Link Dependencies:
- gsl, samtools
- Description:
- The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment.
price¶
- Homepage:
- Spack package:
- Versions:
- 140408
- Description:
- PRICE (Paired-Read Iterative Contig Extension): a de novo genome assembler implemented in C++.
primer3¶
- Homepage:
- Spack package:
- Versions:
- 2.3.7
- Description:
- Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
printproto¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- Xprint extension to the X11 protocol - a portable, network-transparent printing system.
probconsrna¶
- Homepage:
- Spack package:
- Versions:
- 2005-6-7
- Description:
- Experimental version of PROBCONS with parameters estimated via unsupervised training on BRAliBASE
prodigal¶
- Homepage:
- Spack package:
- Versions:
- 2.6.3
- Description:
- Fast, reliable protein-coding gene prediction for prokaryotic genomes.
proj¶
- Homepage:
- Spack package:
- Versions:
- 4.9.2, 4.9.1, 4.8.0, 4.7.0, 4.6.1
- Description:
- Cartographic Projections
protobuf¶
- Homepage:
- Spack package:
- Versions:
- 3.5.1.1, 3.5.1, 3.5.0.1, 3.5.0, 3.4.1, 3.4.0, 3.3.0, 3.2.0, 3.1.0, 3.0.2
- Build Dependencies:
- cmake, zlib
- Link Dependencies:
- zlib
- Description:
- Google's data interchange format.
proxymngr¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- xproto, lbxproxy, util-macros, libxt, pkgconfig, xproxymanagementprotocol, libice
- Link Dependencies:
- lbxproxy, libice, libxt
- Description:
- The proxy manager (proxymngr) is responsible for resolving requests from xfindproxy (and other similar clients), starting new proxies when appropriate, and keeping track of all of the available proxy services. The proxy manager strives to reuse existing proxies whenever possible.
pruners-ninja¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1, 1.0.0
- Build Dependencies:
- automake, autoconf, libtool, mpi
- Link Dependencies:
- mpi
- Description:
- NINJA: Noise Inject agent tool to expose subtle and unintended message races.
ps-lite¶
- Homepage:
- Spack package:
- Versions:
- 20170328, master
- Build Dependencies:
- zeromq, cmake, protobuf
- Link Dependencies:
- zeromq, protobuf
- Description:
- ps-lite is A light and efficient implementation of the parameter server framework.
psi4¶
- Homepage:
- Spack package:
- Versions:
- 0.5
- Build Dependencies:
- py-numpy, boost, lapack, cmake, python, blas
- Link Dependencies:
- lapack, python, boost, blas
- Run Dependencies:
- py-numpy
- Description:
- Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.
pstreams¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Description:
- C++ wrapper for the POSIX.2 functions popen(3) and pclose(3)
pugixml¶
- Homepage:
- Spack package:
- Versions:
- 1.8.1
- Build Dependencies:
- cmake
- Description:
- Light-weight, simple, and fast XML parser for C++ with XPath support
pumi¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.0.1
- Build Dependencies:
- cmake, zoltan, mpi
- Link Dependencies:
- zoltan, mpi
- Description:
- SCOREC RPI's Parallel Unstructured Mesh Infrastructure (PUMI). An efficient distributed mesh data structure and methods to support parallel adaptive analysis including general mesh-based operations, such as mesh entity creation/deletion, adjacency and geometric classification, iterators, arbitrary (field) data attachable to mesh entities, efficient communication involving entities duplicated across multiple tasks, migration of mesh entities between tasks, and dynamic load balancing.
pvm¶
- Homepage:
- Spack package:
- Versions:
- 3.4.6
- Description:
- PVM (Parallel Virtual Machine) is a software package that permits a heterogeneous collection of Unix and/or Windows computers hooked together by a network to be used as a single large parallel computer.
py-3to2¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.
py-4suite-xml¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- XML tools and libraries for Python: Domlette, XPath, XSLT, XPointer, XLink, XUpdate
py-abipy¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- py-numpy, py-pydispatcher, py-setuptools, py-prettytable, py-seaborn, py-matplotlib, py-pyyaml, py-pymatgen, py-six, py-html2text, py-wxmplot, py-scipy, py-jupyter, py-apscheduler, py-netcdf4, py-wxpython, py-ipython, py-cython, py-spglib, py-tqdm, python, py-tabulate, py-pandas, py-nbformat
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pydispatcher, py-prettytable, py-seaborn, py-matplotlib, py-pyyaml, py-pymatgen, py-six, py-html2text, py-wxmplot, py-scipy, py-jupyter, py-apscheduler, py-netcdf4, py-wxpython, py-ipython, py-nbformat, py-spglib, py-tqdm, python, py-tabulate, py-pandas
- Description:
- Python package to automate ABINIT calculations and analyze the results.
py-adios¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
- Build Dependencies:
- py-numpy, mpi, python, py-cython, adios
- Link Dependencies:
- mpi, python, adios
- Run Dependencies:
- py-numpy, py-mpi4py, python, adios
- Description:
- NumPy bindings of ADIOS1
py-alabaster¶
- Homepage:
- Spack package:
- Versions:
- 0.7.10, 0.7.9
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.
py-apache-libcloud¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python library for multiple cloud provider APIs
py-apipkg¶
- Homepage:
- Spack package:
- Versions:
- 1.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- apipkg: namespace control and lazy-import mechanism
py-appdirs¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3, 1.4.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
py-appnope¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Disable App Nap on OS X 10.9
py-apscheduler¶
- Homepage:
- Spack package:
- Versions:
- 3.3.1, 2.1.0
- Build Dependencies:
- py-pytz, python, py-setuptools, py-tzlocal, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-pytz, python, py-tzlocal, py-six
- Description:
- In-process task scheduler with Cron-like capabilities.
py-argcomplete¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Bash tab completion for argparse.
py-argparse¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python command-line parsing library.
py-ase¶
- Homepage:
- Spack package:
- Versions:
- 3.13.0
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
py-asn1crypto¶
- Homepage:
- Spack package:
- Versions:
- 0.22.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python ASN.1 library with a focus on performance and a pythonic API
py-astroid¶
- Homepage:
- Spack package:
- Versions:
- 1.4.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1
- Build Dependencies:
- py-wrapt, py-singledispatch, python, py-backports-functools-lru-cache, py-lazy-object-proxy, py-setuptools, py-six, py-enum34
- Link Dependencies:
- py-wrapt, py-singledispatch, python, py-backports-functools-lru-cache, py-lazy-object-proxy, py-setuptools, py-six, py-enum34
- Run Dependencies:
- python
- Description:
py-astropy¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2, 1.1.post1
- Build Dependencies:
- py-numpy, py-beautifulsoup4, py-scipy, py-markupsafe, py-h5py, py-setuptools, libxml2, py-scikit-image, expat, py-pytz, py-matplotlib, cfitsio, py-pyyaml, python, py-pandas
- Link Dependencies:
- expat, cfitsio, python, libxml2
- Run Dependencies:
- py-numpy, py-markupsafe, py-beautifulsoup4, py-scipy, py-matplotlib, py-scikit-image, py-pytz, py-h5py, python, py-pandas, py-pyyaml
- Description:
- The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.
py-attrs¶
- Homepage:
- Spack package:
- Versions:
- 16.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python Attributes Without Boilerplate
py-autopep8¶
- Homepage:
- Spack package:
- Versions:
- 1.3.3, 1.2.4, 1.2.2
- Build Dependencies:
- python, py-setuptools, py-pycodestyle
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pycodestyle
- Description:
- autopep8 automatically formats Python code to conform to the PEP 8 style guide.
py-babel¶
- Homepage:
- Spack package:
- Versions:
- 2.4.0, 2.3.4
- Build Dependencies:
- py-pytz, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-pytz, python
- Description:
- Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications.
py-backports-abc¶
- Homepage:
- Spack package:
- Versions:
- 0.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Backports_ABC: A backport of recent additions to the 'collections.abc' module.
py-backports-functools-lru-cache¶
- Homepage:
- Spack package:
- Versions:
- 1.4, 1.0.1
- Build Dependencies:
- python, py-setuptools-scm, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Backport of functools.lru_cache from Python 3.3
py-backports-shutil-get-terminal-size¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A backport of the get_terminal_size function from Python 3.3's shutil.
py-backports-ssl-match-hostname¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The ssl.match_hostname() function from Python 3.5
py-basemap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- py-numpy, pil, py-matplotlib, geos, python, py-setuptools
- Link Dependencies:
- geos, python
- Run Dependencies:
- py-numpy, py-matplotlib, python, pil, py-setuptools
- Description:
- The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.
py-beautifulsoup4¶
- Homepage:
- Spack package:
- Versions:
- 4.5.3, 4.5.1, 4.4.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.
py-binwalk¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Binwalk is a fast, easy to use tool for analyzing, reverse engineering, and extracting firmware images.
py-biom-format¶
- Homepage:
- Spack package:
- Versions:
- 2.1.6
- Build Dependencies:
- py-numpy, py-pandas, py-cython, py-scipy, py-click, py-setuptools, py-h5py, python, py-six, py-future
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pandas, py-scipy, py-click, py-h5py, python, py-six, py-future
- Description:
- The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
py-biopython¶
- Homepage:
- Spack package:
- Versions:
- 1.70, 1.65
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- A distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
py-bitarray¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Efficient array of booleans - C extension
py-bleach¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- py-html5lib, python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-html5lib, python, py-six
- Description:
- An easy whitelist-based HTML-sanitizing tool.
py-blessings¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A nicer, kinder way to write to the terminal
py-bokeh¶
- Homepage:
- Spack package:
- Versions:
- 0.12.2
- Build Dependencies:
- py-numpy, py-dateutil, py-six, py-jinja2, py-pyyaml, python, py-tornado, py-futures, py-requests
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-dateutil, py-six, py-jinja2, py-pyyaml, python, py-tornado, py-futures, py-requests
- Description:
- Statistical and novel interactive HTML plots for Python
py-boltons¶
- Homepage:
- Spack package:
- Versions:
- 16.5.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- When they're not builtins, they're boltons. Functionality that should be in the standard library. Like builtins, but Boltons. Otherwise known as, "everyone's util.py," but cleaned up and tested.
py-bottleneck¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- A collection of fast NumPy array functions written in Cython.
py-brian¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3
- Build Dependencies:
- py-numpy, py-matplotlib, python, py-scipy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-scipy
- Description:
- A clock-driven simulator for spiking neural networks
py-brian2¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1, 2.0rc3
- Build Dependencies:
- py-numpy, py-sphinx, py-pyparsing, py-jinja2, py-setuptools, py-cpuinfo, python, py-sympy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-sphinx, py-pyparsing, py-jinja2, py-cpuinfo, python, py-sympy
- Description:
- A clock-driven simulator for spiking neural networks
py-bsddb3¶
- Homepage:
- Spack package:
- Versions:
- 6.2.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python, py-setuptools
- Run Dependencies:
- python
- Description:
- This module provides a nearly complete wrapping of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects, and each of these is exposed as a Python type in the bsddb3.db module.
py-bx-python¶
- Homepage:
- Spack package:
- Versions:
- 0.7.4
- Build Dependencies:
- py-numpy, python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-six
- Description:
- The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
py-cclib¶
- Homepage:
- Spack package:
- Versions:
- 1.5.post1
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Open source library for parsing and interpreting the results of computational chemistry packages
py-cdat-lite¶
- Homepage:
- Spack package:
- Versions:
- 6.0.1
- Build Dependencies:
- netcdf, py-numpy, python, py-setuptools
- Link Dependencies:
- netcdf, python
- Run Dependencies:
- py-numpy, python
- Description:
- Cdat-lite is a Python package for managing and analysing climate science data. It is a subset of the Climate Data Analysis Tools (CDAT) developed by PCMDI at Lawrence Livermore National Laboratory.
py-cdo¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Build Dependencies:
- py-netcdf4, python, py-setuptools, cdo, py-scipy
- Link Dependencies:
- python, cdo
- Run Dependencies:
- py-netcdf4, python, py-scipy
- Description:
- The cdo package provides an interface to the Climate Data Operators from Python.
py-certifi¶
- Homepage:
- Spack package:
- Versions:
- 2017.1.23, 2016.02.28
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts.
py-cffi¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0, 1.1.2
- Build Dependencies:
- py-pycparser, python, py-setuptools, libffi
- Link Dependencies:
- libffi, python
- Run Dependencies:
- py-pycparser, python
- Description:
- Foreign Function Interface for Python calling C code
py-chardet¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Universal encoding detector for Python 2 and 3
py-click¶
- Homepage:
- Spack package:
- Versions:
- 6.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A simple wrapper around optparse for powerful command line utilities.
py-cogent¶
- Homepage:
- Spack package:
- Versions:
- 1.9
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- A toolkit for statistical analysis of biological sequences.
py-colorama¶
- Homepage:
- Spack package:
- Versions:
- 0.3.7
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Cross-platform colored terminal text.
py-colormath¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1
- Build Dependencies:
- py-numpy, python, py-setuptools, py-networkx
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-networkx
- Description:
- Color math and conversion library.
py-configparser¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- This library brings the updated configparser from Python 3.5 to Python 2.6-3.5.
py-counter¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Counter package defines the "counter.Counter" class similar to bags or multisets in other languages.
py-coverage¶
- Homepage:
- Spack package:
- Versions:
- 4.3.4, 4.0a6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Testing coverage checker for python
py-cpuinfo¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Get CPU info with pure Python 2 & 3
py-cryptography¶
- Homepage:
- Spack package:
- Versions:
- 1.8.1
- Build Dependencies:
- py-cffi, py-ipaddress, openssl, py-asn1crypto, py-setuptools, py-idna, python, py-six, py-enum34
- Link Dependencies:
- python, openssl
- Run Dependencies:
- py-cffi, py-ipaddress, py-asn1crypto, py-idna, python, py-six, py-enum34
- Description:
- cryptography is a package which provides cryptographic recipes and primitives to Python developers
py-csvkit¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1
- Build Dependencies:
- py-dateutil, py-xlrd, py-sqlalchemy, py-openpyxl, py-setuptools, py-dbf, python, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-dateutil, py-xlrd, py-sqlalchemy, py-openpyxl, py-dbf, python, py-six
- Description:
- A library of utilities for working with CSV, the king of tabular file formats
py-current¶
- Homepage:
- Spack package:
- Versions:
- 0.3.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Current module relative paths and imports
py-cutadapt¶
- Homepage:
- Spack package:
- Versions:
- 1.13
- Build Dependencies:
- python, py-xopen, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-xopen, python
- Description:
- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
py-cycler¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- Composable style cycles.
py-cython¶
- Homepage:
- Spack package:
- Versions:
- 0.25.2, 0.23.5, 0.23.4, 0.22, 0.21.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The Cython compiler for writing C extensions for the Python language.
py-dask¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Minimal task scheduling abstraction
py-dateutil¶
- Homepage:
- Spack package:
- Versions:
- 2.5.2, 2.4.2, 2.4.0, 2.2
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- Extensions to the standard Python datetime module.
py-dbf¶
- Homepage:
- Spack package:
- Versions:
- 0.96.005, 0.94.003
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)
py-decorator¶
- Homepage:
- Spack package:
- Versions:
- 4.0.9
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.
py-deeptools¶
- Homepage:
- Spack package:
- Versions:
- 2.5.2
- Build Dependencies:
- py-numpy, py-pybigwig, py-numpydoc, py-scipy, py-pysam, py-matplotlib, py-py2bit, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pybigwig, py-numpydoc, py-scipy, py-pysam, py-matplotlib, py-py2bit, python
- Description:
- deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers.
py-dendropy¶
- Homepage:
- Spack package:
- Versions:
- 4.3.0, 3.12.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc.
py-dev¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- libraries and tools for Python development
py-dill¶
- Homepage:
- Spack package:
- Versions:
- 0.2.6, 0.2.5, 0.2.4, 0.2.3, 0.2.2, 0.2.1, 0.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Serialize all of python
py-dlcpar¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- FIXME: Put a proper description of your package here.
py-docutils¶
- Homepage:
- Spack package:
- Versions:
- 0.13.1, 0.12
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man- pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.
py-doxypy¶
- Homepage:
- Spack package:
- Versions:
- 0.3
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- doxypy is an input filter for Doxygen.
py-doxypypy¶
- Homepage:
- Spack package:
- Versions:
- 0.8.8.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Doxygen filter for Python. A more Pythonic version of doxypy, a Doxygen filter for Python.
py-dryscrape¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- py-xvfbwrapper, python, py-lxml, py-webkit-server
- Link Dependencies:
- python
- Run Dependencies:
- py-xvfbwrapper, python, py-lxml, py-webkit-server
- Description:
- a lightweight Javascript-aware, headless web scraping library for Python
py-dxchange¶
- Homepage:
- Spack package:
- Versions:
- 0.1.2
- Build Dependencies:
- py-numpy, py-astropy, py-edffile, py-scipy, py-spefile, py-h5py, py-setuptools, py-dxfile, py-netcdf4, py-tifffile, py-olefile, python, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-astropy, py-edffile, py-scipy, py-spefile, py-h5py, py-dxfile, py-netcdf4, py-tifffile, py-olefile, python, py-six
- Description:
- DXchange provides an interface with tomoPy and raw tomographic data collected at different synchrotron facilities.
py-dxfile¶
- Homepage:
- Spack package:
- Versions:
- 0.4
- Build Dependencies:
- python, py-h5py, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-h5py, python
- Description:
- Scientific Data Exchange [A1] is a set of guidelines for storing scientific data and metadata in a Hierarchical Data Format 5 [B6] file.
py-easybuild-easyblocks¶
- Homepage:
- Spack package:
- Versions:
- 3.1.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python, py-easybuild-framework
- Description:
- Collection of easyblocks for EasyBuild, a software build and installation framework for (scientific) software on HPC systems.
py-easybuild-easyconfigs¶
- Homepage:
- Spack package:
- Versions:
- 3.1.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python, py-easybuild-easyblocks, py-easybuild-framework
- Description:
- Collection of easyconfig files for EasyBuild, a software build and installation framework for (scientific) software on HPC systems.
py-easybuild-framework¶
- Homepage:
- Spack package:
- Versions:
- 3.1.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-vsc-base, py-setuptools, py-vsc-install
- Description:
- The core of EasyBuild, a software build and installation framework for (scientific) software on HPC systems.
py-edffile¶
- Homepage:
- Spack package:
- Versions:
- 5.0.0
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Generic class for Edf files manipulation.
py-editdistance¶
- Homepage:
- Spack package:
- Versions:
- 0.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Fast implementation of the edit distance (Levenshtein distance).
py-elasticsearch¶
- Homepage:
- Spack package:
- Versions:
- 5.2.0, 2.3.0
- Build Dependencies:
- python, py-setuptools, py-urllib3
- Link Dependencies:
- python
- Run Dependencies:
- python, py-urllib3
- Description:
- Python client for Elasticsearch
py-elephant¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1, 0.3.0
- Build Dependencies:
- py-numpy, py-neo, py-numpydoc, py-sphinx, py-scipy, py-quantities, py-setuptools, python, py-pandas
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-neo, py-numpydoc, py-sphinx, py-scipy, py-quantities, python, py-pandas
- Description:
- Elephant is a package for analysis of electrophysiology data in Python
py-emcee¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- emcee is an MIT licensed pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.
py-entrypoints¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3
- Build Dependencies:
- py-configparser, python
- Link Dependencies:
- python
- Run Dependencies:
- py-configparser, python
- Description:
- Discover and load entry points from installed packages.
py-enum34¶
- Homepage:
- Spack package:
- Versions:
- 1.1.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4.
py-epydoc¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings.
py-espresso¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- py-numpy, fftw, boost, mpi, python, cmake, py-cython
- Link Dependencies:
- py-numpy, fftw, boost, mpi, python, py-cython
- Description:
- ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids and biological systems, for example DNA and lipid membranes. It also has a DPD and lattice Boltzmann solver for hydrodynamic interactions, and allows several particle couplings to the LB fluid.
py-espressopp¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.9.5, 1.9.4.1, 1.9.4
- Build Dependencies:
- py-numpy, doxygen, fftw, python, boost, texlive, py-mpi4py, py-matplotlib, py-sphinx, mpi, cmake
- Link Dependencies:
- fftw, python, boost, mpi
- Run Dependencies:
- py-numpy, py-mpi4py
- Description:
- ESPResSo++ is an extensible, flexible, fast and parallel simulation software for soft matter research. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research
py-et-xmlfile¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- An implementation of lxml.xmlfile for the standard library.
py-execnet¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- python, py-setuptools-scm, py-setuptools, py-apipkg
- Link Dependencies:
- python
- Run Dependencies:
- python, py-apipkg
- Description:
- execnet provides a share-nothing model with channel-send/receive communication for distributing execution across many Python interpreters across version, platform and network barriers.
py-fastaindex¶
- Homepage:
- Spack package:
- Versions:
- 0.11rc7
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- FastA index (.fai) handler compatible with samtools faidx is extended with 4 columns storing counts for A, C, G & T for each sequence..
py-fasteners¶
- Homepage:
- Spack package:
- Versions:
- 0.14.1
- Build Dependencies:
- python, py-setuptools, py-monotonic, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-monotonic, py-six
- Description:
- A python package that provides useful locks.
py-faststructure¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- py-numpy, python, gsl, py-cython
- Link Dependencies:
- python, gsl
- Run Dependencies:
- py-numpy, python
- Description:
- FastStructure is a fast algorithm for inferring population structure from large SNP genotype data.
py-fiscalyear¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0, master
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- fiscalyear is a small, lightweight Python module providing helpful utilities for managing the fiscal calendar. It is designed as an extension of the built-in datetime and calendar modules, adding the ability to query the fiscal year and fiscal quarter of a date or datetime object.
py-flake8¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0, 3.0.4, 2.5.4
- Build Dependencies:
- py-configparser, py-mccabe, py-pycodestyle, py-setuptools, py-pyflakes, python, py-enum34
- Link Dependencies:
- python
- Run Dependencies:
- py-configparser, py-mccabe, py-pycodestyle, py-setuptools, py-pyflakes, python, py-enum34
- Description:
- Flake8 is a wrapper around PyFlakes, pep8 and Ned Batchelder's McCabe script.
py-flask¶
- Homepage:
- Spack package:
- Versions:
- 0.12.1, 0.11.1
- Build Dependencies:
- py-werkzeug, py-jinja2, py-click, py-setuptools, py-itsdangerous, python
- Link Dependencies:
- python
- Run Dependencies:
- py-werkzeug, py-click, py-itsdangerous, python, py-jinja2
- Description:
- A microframework based on Werkzeug, Jinja2 and good intentions
py-flexx¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1
- Build Dependencies:
- python, py-setuptools, py-tornado
- Link Dependencies:
- python
- Run Dependencies:
- python, py-tornado
- Description:
- Write desktop and web apps in pure Python.
py-fparser¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.0.6, 0.0.5
- Build Dependencies:
- py-numpy, py-nose, python, py-six, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Test Dependencies:
- py-pytest
- Description:
- Parser for Fortran 77..2003 code.
py-funcsigs¶
- Homepage:
- Spack package:
- Versions:
- 0.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2.
py-functools32¶
- Homepage:
- Spack package:
- Versions:
- 3.2.3-2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy.
py-future¶
- Homepage:
- Spack package:
- Versions:
- 0.16.0, 0.15.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Clean single-source support for Python 3 and 2
py-futures¶
- Homepage:
- Spack package:
- Versions:
- 3.0.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Backport of the concurrent.futures package from Python 3.2
py-genders¶
- Homepage:
- Spack package:
- Versions:
- 1.22
- Build Dependencies:
- python
- Link Dependencies:
- python
- Description:
- Genders is a static cluster configuration database used for cluster configuration management. It is used by a variety of tools and scripts for management of large clusters.
py-genshi¶
- Homepage:
- Spack package:
- Versions:
- 0.7, 0.6.1, 0.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python toolkit for generation of output for the web
py-git-review¶
- Homepage:
- Spack package:
- Versions:
- 1.26.0, 1.25.0, 1.24, 1.23, 1.22, 1.21
- Build Dependencies:
- py-setuptools, py-pbr, python, py-requests
- Link Dependencies:
- python
- Run Dependencies:
- tk, py-pbr, python, py-requests, git
- Description:
- git-review is a tool that helps submitting git branches to gerrit
py-git2¶
- Homepage:
- Spack package:
- Versions:
- 0.24.1
- Build Dependencies:
- python, py-setuptools, libgit2, py-six, py-cffi
- Link Dependencies:
- python, libgit2
- Run Dependencies:
- py-cffi, python, py-six
- Description:
- Pygit2 is a set of Python bindings to the libgit2 shared library, libgit2 implements the core of Git.
py-gnuplot¶
- Homepage:
- Spack package:
- Versions:
- 1.8
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program.
py-griddataformats¶
- Homepage:
- Spack package:
- Versions:
- 0.3.3
- Build Dependencies:
- py-numpy, python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-six
- Description:
- The gridDataFormats package provides classes to unify reading and writing n-dimensional datasets. One can read grid data from files, make them available as a Grid object, and write out the data again.
py-guidata¶
- Homepage:
- Spack package:
- Versions:
- 1.7.5
- Build Dependencies:
- python, py-pyqt, py-h5py, py-setuptools, py-spyder
- Link Dependencies:
- python
- Run Dependencies:
- py-pyqt, py-h5py, python, py-spyder
- Description:
- Automatic graphical user interfaces generation for easy dataset editing and display
py-guiqwt¶
- Homepage:
- Spack package:
- Versions:
- 3.0.2
- Build Dependencies:
- py-numpy, py-pythonqwt, py-scipy, py-guidata, python, py-pillow, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pythonqwt, py-scipy, py-guidata, python, py-pillow
- Description:
- guiqwt is a set of tools for curve and image plotting (extension to PythonQwt)
py-h5py¶
- Homepage:
- Spack package:
- Versions:
- 2.7.1, 2.7.0, 2.6.0, 2.5.0, 2.4.0
- Build Dependencies:
- py-numpy, hdf5, py-cython, mpi, py-setuptools, py-mpi4py, python, py-pkgconfig, py-six
- Link Dependencies:
- hdf5, python, mpi
- Run Dependencies:
- py-numpy, python, py-six, py-mpi4py
- Description:
- The h5py package provides both a high- and low-level interface to the HDF5 library from Python.
py-html2text¶
- Homepage:
- Spack package:
- Versions:
- 2016.9.19
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Turn HTML into equivalent Markdown-structured text.
py-html5lib¶
- Homepage:
- Spack package:
- Versions:
- 0.9999999
- Build Dependencies:
- python, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- HTML parser based on the WHATWG HTML specification.
py-htseq¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1
- Build Dependencies:
- py-numpy, py-cython, py-matplotlib, py-pysam, swig, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-cython, py-matplotlib, py-pysam, swig, python
- Description:
- HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
py-httpbin¶
- Homepage:
- Spack package:
- Versions:
- 0.5.0
- Build Dependencies:
- py-decorator, py-six, py-markupsafe, py-flask, py-itsdangerous, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-decorator, py-markupsafe, py-flask, py-itsdangerous, python, py-six
- Description:
- HTTP Request and Response Service
py-hypothesis¶
- Homepage:
- Spack package:
- Versions:
- 3.7.0
- Build Dependencies:
- python, py-setuptools, py-enum34
- Link Dependencies:
- python
- Run Dependencies:
- python, py-enum34
- Description:
- A library for property based testing.
py-idna¶
- Homepage:
- Spack package:
- Versions:
- 2.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python, py-setuptools
- Run Dependencies:
- python
- Description:
- Internationalized Domain Names for Python (IDNA 2008 and UTS #46)
py-igraph¶
- Homepage:
- Spack package:
- Versions:
- 0.7.0
- Build Dependencies:
- python, py-setuptools, igraph
- Link Dependencies:
- igraph, python
- Run Dependencies:
- python
- Description:
- igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.
py-imagesize¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats.
py-iminuit¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- py-numpy, python, py-setuptools, py-cython, py-matplotlib
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-matplotlib, python
- Description:
- Interactive IPython-Friendly Minimizer based on SEAL Minuit2.
py-importlib¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Packaging for importlib from Python 2.7
py-ipaddress¶
- Homepage:
- Spack package:
- Versions:
- 1.0.18
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python 3.3's ipaddress for older Python versions
py-ipdb¶
- Homepage:
- Spack package:
- Versions:
- 0.10.1
- Build Dependencies:
- py-ipython, py-six, py-prompt-toolkit, py-traitlets, python, py-pexpect, py-setuptools
- Link Dependencies:
- py-ipython, py-prompt-toolkit, py-traitlets, python, py-pexpect, py-six
- Run Dependencies:
- python
- Description:
- ipdb is the iPython debugger and has many additional features, including a better interactive debugging experience via colorized output.
py-ipykernel¶
- Homepage:
- Spack package:
- Versions:
- 4.5.0, 4.4.1, 4.4.0, 4.3.1, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.1, 4.1.0
- Build Dependencies:
- py-ipython, py-jupyter-client, py-pexpect, python, py-traitlets, py-tornado
- Link Dependencies:
- python
- Run Dependencies:
- py-ipython, py-jupyter-client, py-pexpect, python, py-traitlets, py-tornado
- Description:
- IPython Kernel for Jupyter
py-ipython¶
- Homepage:
- Spack package:
- Versions:
- 5.1.0, 3.1.0, 2.3.1
- Build Dependencies:
- py-pickleshare, py-backports-shutil-get-terminal-size, py-pygments, py-simplegeneric, py-prompt-toolkit, py-pexpect, py-decorator, python, py-traitlets, py-pathlib2
- Link Dependencies:
- python
- Run Dependencies:
- py-pickleshare, py-backports-shutil-get-terminal-size, py-pygments, py-simplegeneric, py-prompt-toolkit, py-pexpect, py-decorator, python, py-traitlets, py-pathlib2
- Description:
- IPython provides a rich toolkit to help you make the most out of using Python interactively.
py-ipython-genutils¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Vestigial utilities from IPython
py-ipywidgets¶
- Homepage:
- Spack package:
- Versions:
- 5.2.2
- Build Dependencies:
- python, py-traitlets, py-ipython, py-ipykernel
- Link Dependencies:
- python
- Run Dependencies:
- python, py-traitlets, py-ipython, py-ipykernel
- Description:
- IPython widgets for the Jupyter Notebook
py-isort¶
- Homepage:
- Spack package:
- Versions:
- 4.2.15
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Python utility / library to sort Python imports.
py-itsdangerous¶
- Homepage:
- Spack package:
- Versions:
- 0.24
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Various helpers to pass trusted data to untrusted environments.
py-jdcal¶
- Homepage:
- Spack package:
- Versions:
- 1.3, 1.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Julian dates from proleptic Gregorian and Julian calendars
py-jedi¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0, 0.9.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- An autocompletion tool for Python that can be used for text editors.
py-jinja2¶
- Homepage:
- Spack package:
- Versions:
- 2.9.6, 2.8, 2.7.3, 2.7.2, 2.7.1, 2.7
- Build Dependencies:
- py-markupsafe, py-babel, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-markupsafe, python, py-babel
- Description:
- Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.
py-joblib¶
- Homepage:
- Spack package:
- Versions:
- 0.10.3, 0.10.2, 0.10.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python function as pipeline jobs
py-jpype¶
- Homepage:
- Spack package:
- Versions:
- 0.6.2, 0.6.1, 0.6.0
- Build Dependencies:
- python, py-setuptools, java
- Link Dependencies:
- python
- Run Dependencies:
- java, python
- Description:
- JPype is an effort to allow python programs full access to java class libraries.
py-jsonschema¶
- Homepage:
- Spack package:
- Versions:
- 2.5.1
- Build Dependencies:
- python, py-setuptools, py-vcversioner, py-functools32
- Link Dependencies:
- python
- Run Dependencies:
- python, py-vcversioner, py-functools32
- Description:
- Jsonschema: An(other) implementation of JSON Schema for Python.
py-junit-xml¶
- Homepage:
- Spack package:
- Versions:
- 1.7
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- Creates JUnit XML test result documents that can be read by tools such as Jenkins
py-jupyter-client¶
- Homepage:
- Spack package:
- Versions:
- 4.4.0, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.1, 4.1.0, 4.0.0
- Build Dependencies:
- py-jupyter-core, py-traitlets, python, py-zmq
- Link Dependencies:
- python
- Run Dependencies:
- py-jupyter-core, py-traitlets, python, py-zmq
- Description:
- Jupyter protocol client APIs
py-jupyter-console¶
- Homepage:
- Spack package:
- Versions:
- 5.0.0, 4.1.1, 4.1.0, 4.0.3, 4.0.2
- Build Dependencies:
- py-ipython, py-jupyter-client, py-prompt-toolkit, python, py-pygments, py-ipykernel
- Link Dependencies:
- python
- Run Dependencies:
- py-ipython, py-jupyter-client, py-prompt-toolkit, python, py-pygments, py-ipykernel
- Description:
- Jupyter Terminal Console
py-jupyter-core¶
- Homepage:
- Spack package:
- Versions:
- 4.2.0, 4.1.1, 4.1.0, 4.0.6, 4.0.5, 4.0.4, 4.0.3, 4.0.2, 4.0.1, 4.0
- Build Dependencies:
- py-traitlets, python
- Link Dependencies:
- python
- Run Dependencies:
- py-traitlets, python
- Description:
- Core Jupyter functionality
py-jupyter-notebook¶
- Homepage:
- Spack package:
- Versions:
- 4.2.3, 4.2.2, 4.2.1, 4.2.0, 4.1.0, 4.0.6, 4.0.5, 4.0.4, 4.0.3, 4.0.2
- Build Dependencies:
- py-ipython-genutils, node-js, py-jupyter-core, python, py-traitlets, py-jupyter-console, py-nbconvert, npm, py-ipywidgets, py-jupyter-client, py-jinja2, py-terminado, py-ipykernel, py-tornado, py-nbformat
- Link Dependencies:
- python
- Run Dependencies:
- py-ipython-genutils, node-js, py-jupyter-core, python, py-traitlets, py-jupyter-console, py-nbconvert, py-ipywidgets, py-jupyter-client, py-jinja2, py-terminado, py-ipykernel, py-tornado, py-nbformat
- Description:
- Jupyter Interactive Notebook
py-keras¶
- Homepage:
- Spack package:
- Versions:
- 2.0.3, 1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0
- Build Dependencies:
- python, py-theano, py-setuptools, py-six, py-pyyaml
- Link Dependencies:
- python
- Run Dependencies:
- py-theano, python, py-six, py-pyyaml
- Description:
- Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.
py-latexcodec¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- A lexer and codec to work with LaTeX code in Python.
py-lazy¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Lazy attributes for Python objects
py-lazy-object-proxy¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A fast and thorough lazy object proxy.
py-lazyarray¶
- Homepage:
- Spack package:
- Versions:
- 0.2.10, 0.2.8
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- a Python package that provides a lazily-evaluated numerical array class, larray, based on and compatible with NumPy arrays.
py-libconf¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A pure-Python libconfig reader/writer with permissive license
py-libensemble¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.1.0
- Build Dependencies:
- py-numpy, py-petsc4py, py-scipy, py-mpi4py, py-setuptools, nlopt, python, mpi
- Link Dependencies:
- python, mpi
- Run Dependencies:
- py-numpy, py-petsc4py, py-scipy, py-mpi4py, nlopt, python
- Description:
- Library for managing ensemble-like collections of computations.
py-line-profiler¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- python, py-ipython, py-setuptools, py-cython
- Link Dependencies:
- python
- Run Dependencies:
- py-ipython, python
- Description:
- Line-by-line profiler.
py-linecache2¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- python, py-pbr, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-pbr, python
- Description:
- Backports of the linecache module
py-lit¶
- Homepage:
- Spack package:
- Versions:
- 0.5.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures. lit is designed to be a lightweight testing tool with as simple a user interface as possible.
py-llvmlite¶
- Homepage:
- Spack package:
- Versions:
- 0.20.0
- Build Dependencies:
- python, llvm, py-setuptools, binutils, py-enum34
- Link Dependencies:
- llvm, python
- Run Dependencies:
- python, py-enum34
- Description:
- A lightweight LLVM python binding for writing JIT compilers
py-lmfit¶
- Homepage:
- Spack package:
- Versions:
- 0.9.5
- Build Dependencies:
- py-numpy, python, py-setuptools, py-scipy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- Least-Squares Minimization with Bounds and Constraints
py-localcider¶
- Homepage:
- Spack package:
- Versions:
- 0.1.14
- Build Dependencies:
- py-numpy, python, py-setuptools, py-scipy, py-matplotlib
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-scipy
- Description:
- Tools for calculating sequence properties of disordered proteins
py-lockfile¶
- Homepage:
- Spack package:
- Versions:
- 0.10.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The lockfile package exports a LockFile class which provides a simple API for locking files. Unlike the Windows msvcrt.locking function, the fcntl.lockf and flock functions, and the deprecated posixfile module, the API is identical across both Unix (including Linux and Mac) and Windows platforms. The lock mechanism relies on the atomic nature of the link (on Unix) and mkdir (on Windows) system calls. An implementation based on SQLite is also provided, more as a demonstration of the possibilities it provides than as production-quality code.
py-logilab-common¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- Common modules used by Logilab projects
py-lrudict¶
- Homepage:
- Spack package:
- Versions:
- 1.1.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A fast LRU cache
py-lxml¶
- Homepage:
- Spack package:
- Versions:
- 3.7.3, 2.3
- Build Dependencies:
- libxslt, python, py-setuptools, py-cython, libxml2
- Link Dependencies:
- python
- Run Dependencies:
- libxslt, python, libxml2
- Description:
- lxml is the most feature-rich and easy-to-use library for processing XML and HTML in the Python language.
py-lzstring¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- python, py-setuptools, py-future
- Link Dependencies:
- python
- Run Dependencies:
- python, py-future
- Description:
- lz-string for python.
py-macholib¶
- Homepage:
- Spack package:
- Versions:
- 1.8
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python package for Mach-O header analysis and editing
py-machotools¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- python, py-macholib, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-macholib, python
- Description:
- Python package for editing Mach-O headers using macholib
py-macs2¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1.20160309
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-setuptools
- Description:
- MACS2 Model-based Analysis of ChIP-Seq
py-mako¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4, 1.0.1
- Build Dependencies:
- py-markupsafe, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-markupsafe, python
- Description:
- A super-fast templating language that borrows the best ideas from the existing templating languages.
py-mappy¶
- Homepage:
- Spack package:
- Versions:
- 2.2
- Build Dependencies:
- python, zlib
- Link Dependencies:
- python, zlib
- Run Dependencies:
- python
- Description:
- Mappy provides a convenient interface to minimap2.
py-markdown¶
- Homepage:
- Spack package:
- Versions:
- 2.6.7, 2.6.6, 2.6.5, 2.6.4, 2.6.3, 2.6.2, 2.6.1, 2.6, 2.5.2, 2.5.1, 2.5
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few very minor differences. See John's Syntax Documentation for the syntax rules.
py-markupsafe¶
- Homepage:
- Spack package:
- Versions:
- 1.0, 0.23, 0.22, 0.21, 0.20, 0.19
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escaping rules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine, the Pylons web framework and many more.
py-matplotlib¶
- Homepage:
- Spack package:
- Versions:
- 2.0.2, 2.0.0, 1.5.3, 1.5.1, 1.4.3, 1.4.2
- Build Dependencies:
- libpng, py-numpy, py-dateutil, py-subprocess32, py-pyparsing, pkgconfig, python, qt, py-setuptools, py-functools32, tk, qhull, freetype, py-pyside, py-ipython, py-pytz, pil, py-cycler, py-six, image-magick
- Link Dependencies:
- libpng, qhull, freetype, tk, qt, python, image-magick
- Run Dependencies:
- py-numpy, py-dateutil, py-subprocess32, ghostscript, py-pyparsing, texlive, python, py-pyside, py-setuptools, py-functools32, py-cycler, py-ipython, py-pytz, pil, py-six
- Description:
- matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.
py-mccabe¶
- Homepage:
- Spack package:
- Versions:
- 0.6.1, 0.6.0, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.0, 0.3.1, 0.3, 0.2.1, 0.2, 0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Ned's script to check McCabe complexity.
py-mdanalysis¶
- Homepage:
- Spack package:
- Versions:
- 0.15.0
- Build Dependencies:
- py-numpy, py-biopython, py-scipy, py-setuptools, py-griddataformats, py-netcdf4, py-seaborn, py-cython, py-networkx, py-matplotlib, python, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-netcdf4, py-seaborn, hdf5, py-biopython, py-scipy, py-networkx, py-matplotlib, python, py-six, py-griddataformats
- Description:
- MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)
py-meep¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2
- Build Dependencies:
- py-numpy, python, py-scipy, mpi, py-matplotlib, swig, meep
- Link Dependencies:
- swig, python, meep, mpi
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-scipy
- Description:
- Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python
py-memory-profiler¶
- Homepage:
- Spack package:
- Versions:
- 0.47
- Build Dependencies:
- python, py-setuptools, py-psutil
- Link Dependencies:
- python
- Run Dependencies:
- py-psutil, python
- Description:
- A module for monitoring memory usage of a python program
py-methylcode¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- py-numpy, py-pyparsing, bowtie, py-setuptools, py-bsddb3, python, py-pyfasta, py-six
- Link Dependencies:
- py-numpy, py-pyparsing, bowtie, py-setuptools, py-bsddb3, python, py-pyfasta, py-six
- Run Dependencies:
- python
- Description:
- MethylCoder is a single program that takes of bisulfite-treated reads and outputs per-base methylation data.
py-misopy¶
- Homepage:
- Spack package:
- Versions:
- 0.5.4
- Build Dependencies:
- py-numpy, samtools, py-scipy, bedtools2, py-pysam, py-matplotlib, python, py-setuptools
- Link Dependencies:
- python, samtools, bedtools2
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-scipy, py-pysam
- Description:
- MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
py-mistune¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1, 0.7, 0.6, 0.5.1, 0.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python markdown parser
py-mock¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0, 1.3.0
- Build Dependencies:
- python, py-pbr, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-pbr, python
- Description:
- mock is a library for testing in Python. It allows you to replace parts of your system under test with mock objects and make assertions about how they have been used.
py-moltemplate¶
- Homepage:
- Spack package:
- Versions:
- 2.5.8
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- Moltemplate is a general cross-platform text-based molecule builder for LAMMPS.
py-mongo¶
- Homepage:
- Spack package:
- Versions:
- 3.6.0, 3.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python driver for MongoDB <http://www.mongodb.org>
py-monotonic¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- An implementation of time.monotonic() for Python 2 & < 3.3
py-monty¶
- Homepage:
- Spack package:
- Versions:
- 0.9.6
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- Monty is the missing complement to Python.
py-mpi4py¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.0.0, 2.0.0, 1.3.1
- Build Dependencies:
- python, py-setuptools, py-cython, mpi
- Link Dependencies:
- python, mpi
- Run Dependencies:
- python
- Description:
- This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.
py-mpmath¶
- Homepage:
- Spack package:
- Versions:
- 0.19
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Python library for arbitrary-precision floating-point arithmetic.
py-multiprocess¶
- Homepage:
- Spack package:
- Versions:
- 0.70.5, 0.70.4
- Build Dependencies:
- python, py-setuptools, py-dill
- Link Dependencies:
- python
- Run Dependencies:
- python, py-dill
- Description:
- Better multiprocessing and multithreading in Python
py-multiqc¶
- Homepage:
- Spack package:
- Versions:
- 1.3, 1.0
- Build Dependencies:
- py-lzstring, py-numpy, py-future, py-jinja2, py-click, py-matplotlib, py-simplejson, python, py-spectra, py-setuptools, py-pyyaml
- Link Dependencies:
- python
- Run Dependencies:
- py-lzstring, py-numpy, py-future, py-jinja2, py-click, py-matplotlib, py-simplejson, python, py-spectra, py-pyyaml
- Description:
- MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools.
py-mx¶
- Homepage:
- Spack package:
- Versions:
- 3.2.8
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types.
py-mxnet¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0.post2
- Build Dependencies:
- py-numpy, python, py-setuptools, mxnet
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-setuptools, mxnet
- Description:
- Python binding for DMLC/MXNet.
py-myhdl¶
- Homepage:
- Spack package:
- Versions:
- 0.9.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python as a Hardware Description Language
py-mysqldb1¶
- Homepage:
- Spack package:
- Versions:
- 1.2.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Legacy mysql bindings for python
py-nbconvert¶
- Homepage:
- Spack package:
- Versions:
- 4.2.0, 4.1.0, 4.0.0
- Build Dependencies:
- py-entrypoints, py-jupyter-core, py-pycurl, py-mistune, py-nbformat, py-jupyter-client, py-jinja2, py-traitlets, python, py-pygments, py-tornado
- Link Dependencies:
- python
- Run Dependencies:
- py-entrypoints, py-jupyter-core, py-mistune, py-nbformat, py-jupyter-client, py-jinja2, py-traitlets, python, py-pygments, py-tornado
- Description:
- Jupyter Notebook Conversion
py-nbformat¶
- Homepage:
- Spack package:
- Versions:
- 4.1.0, 4.0.1, 4.0.0
- Build Dependencies:
- py-jupyter-core, py-traitlets, py-jsonschema, python, py-ipython-genutils
- Link Dependencies:
- python
- Run Dependencies:
- py-jupyter-core, py-traitlets, py-jsonschema, python, py-ipython-genutils
- Description:
- The Jupyter Notebook format
py-neo¶
- Homepage:
- Spack package:
- Versions:
- 0.5.2, 0.4.1
- Build Dependencies:
- py-numpy, python, py-setuptools, py-quantities
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-quantities
- Description:
- Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats
py-nestle¶
- Homepage:
- Spack package:
- Versions:
- 0.1.1
- Build Dependencies:
- py-numpy, python, py-scipy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- Nested sampling algorithms for evaluating Bayesian evidence.
py-netcdf4¶
- Homepage:
- Spack package:
- Versions:
- 1.2.7, 1.2.3.1
- Build Dependencies:
- py-numpy, netcdf, hdf5, py-cython, py-setuptools, python
- Link Dependencies:
- netcdf, hdf5, python
- Run Dependencies:
- py-numpy, python
- Description:
- Python interface to the netCDF Library.
py-netifaces¶
- Homepage:
- Spack package:
- Versions:
- 0.10.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Portable network interface information
py-networkx¶
- Homepage:
- Spack package:
- Versions:
- 1.11, 1.10
- Build Dependencies:
- python, py-decorator, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-decorator, python
- Description:
- NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
py-nose¶
- Homepage:
- Spack package:
- Versions:
- 1.3.7, 1.3.6, 1.3.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- nose extends the test loading and running features of unittest, making it easier to write, find and run tests.
py-nosexcover¶
- Homepage:
- Spack package:
- Versions:
- 1.0.11
- Build Dependencies:
- python, py-setuptools, py-coverage, py-nose
- Link Dependencies:
- python
- Run Dependencies:
- py-nose, python, py-coverage
- Description:
- A companion to the built-in nose.plugins.cover, this plugin will write out an XML coverage report to a file named coverage.xml.
py-numba¶
- Homepage:
- Spack package:
- Versions:
- 0.35.0
- Build Dependencies:
- py-numpy, py-singledispatch, py-funcsigs, python, py-llvmlite, py-argparse
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-singledispatch, py-funcsigs, python, py-llvmlite, py-argparse
- Description:
- NumPy aware dynamic Python compiler using LLVM
py-numexpr¶
- Homepage:
- Spack package:
- Versions:
- 2.6.1, 2.5, 2.4.6
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Fast numerical expression evaluator for NumPy
py-numpy¶
- Homepage:
- Spack package:
- Versions:
- 1.13.3, 1.13.1, 1.13.0, 1.12.1, 1.12.0, 1.11.2, 1.11.1, 1.11.0, 1.10.4, 1.9.2, 1.9.1
- Build Dependencies:
- lapack, python, py-setuptools, blas
- Link Dependencies:
- lapack, python, blas
- Run Dependencies:
- python
- Description:
- NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities
py-numpydoc¶
- Homepage:
- Spack package:
- Versions:
- 0.6.0
- Build Dependencies:
- python, py-setuptools, py-sphinx
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- numpydoc - Numpy's Sphinx extensions
py-olefile¶
- Homepage:
- Spack package:
- Versions:
- 0.44
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python package to parse, read and write Microsoft OLE2 files
py-ont-fast5-api¶
- Homepage:
- Spack package:
- Versions:
- 0.3.2
- Build Dependencies:
- py-numpy, python, py-h5py, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-h5py, python
- Description:
- This project provides classes and utility functions for working with read fast5 files. It provides an abstraction layer between the underlying h5py library and the various concepts central to read fast5 files, such as "reads", "analyses", "analysis summaries", and "analysis datasets". Ideally all interaction with a read fast5 file should be possible via this API, without having to directly invoke the h5py library.
py-openpmd-validator¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0.2
- Build Dependencies:
- py-numpy, python, py-dateutil, py-h5py, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-dateutil, py-h5py, python
- Description:
- Validator and Example Scripts for the openPMD markup. openPMD is an open standard for particle-mesh data files.
py-openpyxl¶
- Homepage:
- Spack package:
- Versions:
- 2.4.5, 2.2.0-b1
- Build Dependencies:
- python, py-setuptools, py-et-xmlfile, py-jdcal
- Link Dependencies:
- python
- Run Dependencies:
- python, py-et-xmlfile, py-jdcal
- Description:
- A Python library to read/write Excel 2010 xlsx/xlsm files
py-ordereddict¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A drop-in substitute for Py2.7's new collections. OrderedDict that works in Python 2.4-2.6.
py-oset¶
- Homepage:
- Spack package:
- Versions:
- 0.1.3
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Set that remembers original insertion order.
py-packaging¶
- Homepage:
- Spack package:
- Versions:
- 16.8
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six, py-pyparsing
- Description:
- Core utilities for Python packages.
py-palettable¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Color palettes for Python.
py-pandas¶
- Homepage:
- Spack package:
- Versions:
- 0.21.1, 0.19.2, 0.19.0, 0.18.0, 0.16.1, 0.16.0
- Build Dependencies:
- py-numpy, py-pytz, py-dateutil, py-cython, py-numexpr, py-setuptools, py-bottleneck, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pytz, py-dateutil, py-numexpr, py-bottleneck, python
- Description:
- pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language.
py-paramiko¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2
- Build Dependencies:
- py-pyasn1, python, py-setuptools, py-cryptography
- Link Dependencies:
- python
- Run Dependencies:
- py-pyasn1, py-cryptography, python
- Description:
- SSH2 protocol library
py-pathlib2¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Backport of pathlib from python 3.4
py-pathos¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- py-pox, python, py-ppft, py-setuptools, py-dill, py-multiprocess
- Link Dependencies:
- python
- Run Dependencies:
- py-pox, python, py-ppft, py-multiprocess, py-dill
- Description:
- Parallel graph management and execution in heterogeneous computing
py-pathspec¶
- Homepage:
- Spack package:
- Versions:
- 0.3.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- pathspec extends the test loading and running features of unittest, making it easier to write, find and run tests.
py-patsy¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1
- Build Dependencies:
- py-numpy, python, py-setuptools, py-scipy, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-scipy, py-six
- Description:
- A Python package for describing statistical models and for building design matrices.
py-pbr¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0, 1.8.1
- Build Dependencies:
- python, py-setuptools, py-enum34
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- PBR is a library that injects some useful and sensible default behaviors into your setuptools run.
py-periodictable¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- py-numpy, python, py-setuptools, py-pyparsing
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-pyparsing
- Description:
- nose extends the test loading and running features of unittest, making it easier to write, find and run tests.
py-petsc4py¶
- Homepage:
- Spack package:
- Versions:
- 3.8.1, 3.8.0, 3.7.0
- Build Dependencies:
- py-numpy, petsc, python, py-setuptools, py-mpi4py
- Link Dependencies:
- python, petsc
- Run Dependencies:
- py-numpy, python, py-mpi4py
- Description:
- This package provides Python bindings for the PETSc package.
py-pexpect¶
- Homepage:
- Spack package:
- Versions:
- 4.2.1, 3.3
- Build Dependencies:
- py-ptyprocess, python
- Link Dependencies:
- python
- Run Dependencies:
- py-ptyprocess, python
- Description:
- Pexpect allows easy control of interactive console applications.
py-phonopy¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0
- Build Dependencies:
- py-numpy, py-matplotlib, python, py-scipy, py-pyyaml
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-scipy, py-pyyaml
- Description:
- Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.
py-pil¶
- Homepage:
- Spack package:
- Versions:
- 1.1.7
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.
py-pillow¶
- Homepage:
- Spack package:
- Versions:
- 3.3.0.dev0, 3.2.0, 3.0.0
- Build Dependencies:
- openjpeg, binutils, zlib, lcms, py-setuptools, libtiff, python, jpeg, freetype
- Link Dependencies:
- openjpeg, zlib, lcms, freetype, libtiff, python, jpeg
- Run Dependencies:
- python
- Description:
- Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.
py-pip¶
- Homepage:
- Spack package:
- Versions:
- 9.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- The PyPA recommended tool for installing Python packages.
py-pipits¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- py-numpy, fastx-toolkit, java, rdp-classifier, py-biom-format, hmmer, python, vsearch, itsx
- Link Dependencies:
- fastx-toolkit, rdp-classifier, itsx, hmmer, python, vsearch
- Run Dependencies:
- py-numpy, python, py-biom-format, java
- Description:
- Automated pipeline for analyses of fungal ITS from the Illumina
py-pkgconfig¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- pkgconfig, python
- Description:
- Interface Python with pkg-config.
py-plotly¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- py-pytz, python, py-setuptools, py-requests, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-pytz, python, py-requests, py-six
- Description:
- An interactive, browser-based graphing library for Python
py-ply¶
- Homepage:
- Spack package:
- Versions:
- 3.8
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- PLY is nothing more than a straightforward lex/yacc implementation.
py-pmw¶
- Homepage:
- Spack package:
- Versions:
- 2.0.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts.
py-pox¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3, 0.2.2, 0.2.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Utilities for filesystem exploration and automated builds.
py-ppft¶
- Homepage:
- Spack package:
- Versions:
- 1.6.4.7.1, 1.6.4.6, 1.6.4.5
- Build Dependencies:
- python, py-setuptools, py-dill, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-dill, py-six
- Description:
- Distributed and parallel python
py-prettytable¶
- Homepage:
- Spack package:
- Versions:
- 0.7.2
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data in visually appealing ASCII tables.
py-proj¶
- Homepage:
- Spack package:
- Versions:
- 1.9.5.1.1, 1.9.5.1
- Build Dependencies:
- python, py-setuptools, py-cython
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python interface to the PROJ.4 Library.
py-prompt-toolkit¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- python, py-setuptools, py-six, py-wcwidth
- Link Dependencies:
- python
- Run Dependencies:
- py-wcwidth, python, py-six
- Description:
- Library for building powerful interactive command lines in Python
py-protobuf¶
- Homepage:
- Spack package:
- Versions:
- 3.0.0b2, 2.6.1, 2.5.0, 2.4.1, 2.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages.
py-psutil¶
- Homepage:
- Spack package:
- Versions:
- 5.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- psutil is a cross-platform library for retrieving information on running processes and system utilization (CPU, memory, disks, network) in Python.
py-psyclone¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.5.1
- Build Dependencies:
- py-setuptools, python, py-fparser, py-pyparsing
- Link Dependencies:
- python
- Run Dependencies:
- python, py-fparser, py-pyparsing
- Test Dependencies:
- py-numpy, py-nose, py-pytest
- Description:
- Code generation for the PSyKAl framework from the GungHo project, as used by the LFRic model at the UK Met Office.
py-ptyprocess¶
- Homepage:
- Spack package:
- Versions:
- 0.5.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Run a subprocess in a pseudo terminal
py-pudb¶
- Homepage:
- Spack package:
- Versions:
- 2017.1.1, 2016.2
- Build Dependencies:
- python, py-setuptools, py-pygments, py-urwid
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools, py-pygments, py-urwid
- Description:
- Full-screen console debugger for Python
py-py¶
- Homepage:
- Spack package:
- Versions:
- 1.4.33, 1.4.31
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- library with cross-python path, ini-parsing, io, code, log facilities
py-py2bit¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A package for accessing 2bit files using lib2bit.
py-py2cairo¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0
- Build Dependencies:
- pkgconfig, python, cairo, pixman
- Link Dependencies:
- python, cairo, pixman
- Run Dependencies:
- python
- Description:
- Pycairo is a set of Python bindings for the cairo graphics library.
py-py2neo¶
- Homepage:
- Spack package:
- Versions:
- 2.0.8, 2.0.7, 2.0.6, 2.0.5, 2.0.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Py2neo is a client library and toolkit for working with Neo4j from within Python applications and from the command line.
py-py4j¶
- Homepage:
- Spack package:
- Versions:
- 0.10.4, 0.10.3
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Enables Python programs to dynamically access arbitrary Java objects.
py-pyani¶
- Homepage:
- Spack package:
- Versions:
- 0.2.7, 0.2.6
- Build Dependencies:
- py-seaborn, py-pandas, py-biopython, py-scipy, py-matplotlib, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-seaborn, python, py-biopython, py-scipy, blast-plus, py-matplotlib, mummer, py-pandas
- Description:
- pyani is a Python3 module that provides support for calculating average nucleotide identity (ANI) and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.
py-pyasn1¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Generic ASN.1 library for Python http://pyasn1.sf.net
py-pybedtools¶
- Homepage:
- Spack package:
- Versions:
- 0.7.10
- Build Dependencies:
- py-numpy, py-pandas, bedtools2, py-pysam, py-setuptools, python, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pandas, bedtools2, py-pysam, python, py-six
- Description:
- pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
py-pybigwig¶
- Homepage:
- Spack package:
- Versions:
- 0.3.4
- Build Dependencies:
- python, curl, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- curl, python
- Description:
- A package for accessing bigWig files using libBigWig.
py-pybind11¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.1, 2.1.0
- Build Dependencies:
- cmake, python, py-pytest
- Link Dependencies:
- python
- Description:
- pybind11 -- Seamless operability between C++11 and Python. pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.
py-pybtex¶
- Homepage:
- Spack package:
- Versions:
- 0.21
- Build Dependencies:
- python, py-latexcodec, py-setuptools, py-pyyaml
- Link Dependencies:
- python
- Run Dependencies:
- py-latexcodec, python, py-pyyaml
- Description:
- Pybtex is a BibTeX-compatible bibliography processor written in Python.
py-pybtex-docutils¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1
- Build Dependencies:
- py-docutils, python, py-setuptools, py-six, py-pybtex
- Link Dependencies:
- python
- Run Dependencies:
- python, py-docutils, py-six, py-pybtex
- Description:
- A docutils backend for pybtex.
py-pychecker¶
- Homepage:
- Spack package:
- Versions:
- 0.8.19
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python source code checking tool.
py-pycodestyle¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1, 2.3.0, 2.2.0, 2.1.0, 2.0.0, 1.7.0, 1.6.2, 1.6.1, 1.6, 1.5.7, 1.5.6, 1.5.5, 1.5.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8. Note: formerly called pep8.
py-pycparser¶
- Homepage:
- Spack package:
- Versions:
- 2.17, 2.13
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A complete parser of the C language, written in pure python.
py-pycrypto¶
- Homepage:
- Spack package:
- Versions:
- 2.6.1
- Build Dependencies:
- python, gmp
- Link Dependencies:
- python, gmp
- Run Dependencies:
- python
- Description:
- The Python Cryptography Toolkit
py-pycurl¶
- Homepage:
- Spack package:
- Versions:
- 7.43.0
- Build Dependencies:
- curl, python
- Link Dependencies:
- curl, python
- Run Dependencies:
- python
- Description:
- PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program.
py-pydatalog¶
- Homepage:
- Spack package:
- Versions:
- 0.17.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- pyDatalog adds logic programming to Python.
py-pydispatcher¶
- Homepage:
- Spack package:
- Versions:
- 2.0.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Multi-producer-multi-consumer signal dispatching mechanism.
py-pydot¶
- Homepage:
- Spack package:
- Versions:
- 1.2.3, 1.2.2
- Build Dependencies:
- python, py-setuptools, py-pyparsing, graphviz
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pyparsing, graphviz
- Description:
- Python interface to Graphviz's Dot language
py-pyelftools¶
- Homepage:
- Spack package:
- Versions:
- 0.23
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A pure-Python library for parsing and analyzing ELF files and DWARF debugging information
py-pyfasta¶
- Homepage:
- Spack package:
- Versions:
- 0.5.2
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- py-numpy, python, py-setuptools
- Run Dependencies:
- python
- Description:
- Pyfasta: fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
py-pyfftw¶
- Homepage:
- Spack package:
- Versions:
- 0.10.4
- Build Dependencies:
- py-numpy, fftw, py-cython, py-scipy, py-setuptools, python
- Link Dependencies:
- fftw, python
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.
py-pyflakes¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0, 1.5.0, 1.4.0, 1.3.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0, 1.0.0, 0.9.2, 0.9.1, 0.9.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- A simple program which checks Python source files for errors.
py-pygments¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.3, 2.0.2, 2.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Pygments is a syntax highlighting package written in Python.
py-pygobject¶
- Homepage:
- Spack package:
- Versions:
- 2.28.6, 2.28.3
- Build Dependencies:
- py-py2cairo, gobject-introspection, python, libffi, glib
- Link Dependencies:
- gobject-introspection, python, libffi, glib
- Run Dependencies:
- py-py2cairo
- Description:
- bindings for the GLib, and GObject, to be used in Python.
py-pygtk¶
- Homepage:
- Spack package:
- Versions:
- 2.24.0
- Build Dependencies:
- py-py2cairo, gtkplus, libffi, cairo, python, glib, py-pygobject
- Link Dependencies:
- python, gtkplus, libffi, cairo, glib
- Run Dependencies:
- py-py2cairo, py-pygobject
- Description:
- bindings for the Gtk2 in Python. use pygobject for Gtk3.
py-pylint¶
- Homepage:
- Spack package:
- Versions:
- 1.6.5, 1.4.3, 1.4.1
- Build Dependencies:
- py-singledispatch, python, py-configparser, py-mccabe, py-isort, py-astroid, py-editdistance, py-backports-functools-lru-cache, py-setuptools, py-six
- Link Dependencies:
- py-singledispatch, py-configparser, py-mccabe, py-editdistance, py-backports-functools-lru-cache, python, py-isort
- Run Dependencies:
- python, py-astroid, py-six
- Description:
- array processing for numbers, strings, records, and objects.
py-pymatgen¶
- Homepage:
- Spack package:
- Versions:
- 4.7.2, 4.6.2
- Build Dependencies:
- py-numpy, py-monty, py-pydispatcher, py-scipy, py-palettable, py-setuptools, py-tabulate, py-pyyaml, py-spglib, py-matplotlib, python, py-requests, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-monty, py-pydispatcher, py-scipy, py-palettable, py-requests, py-spglib, py-matplotlib, py-pyyaml, python, py-tabulate, py-six
- Description:
- Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project.
py-pyminifier¶
- Homepage:
- Spack package:
- Versions:
- 2.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Pyminifier is a Python code minifier, obfuscator, and compressor.
py-pympler¶
- Homepage:
- Spack package:
- Versions:
- 0.4.3, 0.4.2, 0.4.1, 0.4, 0.3.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Development tool to measure, monitor and analyze the memory behavior of Python objects in a running Python application.
py-pynn¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1, 0.8.3, 0.8.1, 0.8beta, 0.7.5
- Build Dependencies:
- py-numpy, py-neo, py-docutils, py-lazyarray, py-jinja2, python, py-quantities
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-neo, py-docutils, py-lazyarray, py-jinja2, python, py-quantities
- Description:
- A Python package for simulator-independent specification of neuronal network models
py-pypar¶
- Homepage:
- Spack package:
- Versions:
- 2.1.5_108
- Build Dependencies:
- py-numpy, python, mpi
- Link Dependencies:
- python, mpi
- Run Dependencies:
- py-numpy, python
- Description:
- Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel on multiple processors and communicate using MPI.
py-pyparsing¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0, 2.1.10, 2.0.3
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Python Parsing Module.
py-pypeflow¶
- Homepage:
- Spack package:
- Versions:
- 2017-05-04
- Build Dependencies:
- python, py-setuptools, py-networkx
- Link Dependencies:
- python
- Run Dependencies:
- python, py-networkx
- Description:
- pypeFLOW is light weight and reusable make / flow data process library written in Python.
py-pyprof2html¶
- Homepage:
- Spack package:
- Versions:
- 0.3.1
- Build Dependencies:
- python, py-setuptools, py-jinja2
- Link Dependencies:
- python
- Run Dependencies:
- python, py-jinja2
- Description:
- Python cProfile and hotshot profile's data to HTML Converter
py-pyqt¶
- Homepage:
- Spack package:
- Versions:
- 4.11.3
- Build Dependencies:
- py-sip, python, qt
- Link Dependencies:
- qt, python
- Run Dependencies:
- py-sip
- Description:
- PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework and runs on all platforms supported by Qt including Windows, MacOS/X and Linux.
py-pyrad¶
- Homepage:
- Spack package:
- Versions:
- 3.0.66
- Build Dependencies:
- py-numpy, muscle, py-scipy, python, py-setuptools, vsearch
- Link Dependencies:
- muscle, python, vsearch
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- RADseq for phylogenetics & introgression analyses
py-pysam¶
- Homepage:
- Spack package:
- Versions:
- 0.13, 0.11.2.2, 0.7.7
- Build Dependencies:
- bcftools, python, py-setuptools, py-cython
- Link Dependencies:
- bcftools, python
- Run Dependencies:
- python
- Description:
- A python module for reading, manipulating and writing genomic data sets.
py-pyscaf¶
- Homepage:
- Spack package:
- Versions:
- 0.12a4
- Build Dependencies:
- python, py-setuptools, py-fastaindex
- Link Dependencies:
- python
- Run Dependencies:
- py-fastaindex, python
- Description:
- pyScaf orders contigs from genome assemblies utilising several types of information
py-pyserial¶
- Homepage:
- Spack package:
- Versions:
- 3.1.1
- Build Dependencies:
- py-setuptools
- Description:
- Python Serial Port Extension
py-pyside¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4, 1.2.2
- Build Dependencies:
- py-sphinx, libxslt, python, qt, cmake, py-setuptools, libxml2
- Link Dependencies:
- libxslt, qt, python, libxml2
- Run Dependencies:
- python, py-sphinx
- Description:
- Python bindings for Qt.
py-pysocks¶
- Homepage:
- Spack package:
- Versions:
- 1.6.6, 1.5.7
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Python SOCKS client module.
py-pytables¶
- Homepage:
- Spack package:
- Versions:
- 3.3.0, 3.2.2
- Build Dependencies:
- py-numpy, hdf5, py-cython, py-numexpr, python, py-setuptools, py-six
- Link Dependencies:
- hdf5, python
- Run Dependencies:
- py-numpy, py-numexpr, python, py-cython, py-six
- Description:
- PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.
py-pytest¶
- Homepage:
- Spack package:
- Versions:
- 3.0.7, 3.0.2
- Build Dependencies:
- python, py-hypothesis, py-setuptools, py-py
- Link Dependencies:
- python
- Run Dependencies:
- python, py-hypothesis, py-setuptools, py-py
- Description:
- pytest: simple powerful testing with Python.
py-pytest-cov¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1
- Build Dependencies:
- python, py-setuptools, py-pytest, py-coverage
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pytest, py-coverage
- Description:
- Pytest plugin for measuring coverage.
py-pytest-flake8¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1
- Build Dependencies:
- python, py-setuptools, py-pytest, py-flake8
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pytest, py-flake8
- Description:
- pytest plugin to check FLAKE8 requirements.
py-pytest-httpbin¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3
- Build Dependencies:
- py-six, py-flask, py-decorator, python, py-httpbin, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-flask, py-decorator, python, py-httpbin, py-six
- Description:
- Easily test your HTTP library against a local copy of httpbin
py-pytest-mock¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- python, py-mock, py-setuptools, py-pytest
- Link Dependencies:
- python
- Run Dependencies:
- py-mock, python, py-pytest
- Description:
- Thin-wrapper around the mock package for easier use with py.test
py-pytest-runner¶
- Homepage:
- Spack package:
- Versions:
- 2.11.1
- Build Dependencies:
- python, py-setuptools-scm, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Invoke py.test as distutils command with dependency resolution.
py-pytest-xdist¶
- Homepage:
- Spack package:
- Versions:
- 1.16.0
- Build Dependencies:
- python, py-execnet, py-setuptools, py-pytest, py-py
- Link Dependencies:
- python
- Run Dependencies:
- py-execnet, python, py-pytest, py-py
- Description:
- py.test xdist plugin for distributed testing and loop-on-failing mode
py-python-daemon¶
- Homepage:
- Spack package:
- Versions:
- 2.0.5
- Build Dependencies:
- python, py-lockfile, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-lockfile, python
- Description:
- Library to implement a well-behaved Unix daemon process. This library implements the well-behaved daemon specification of PEP Standard daemon process. A well-behaved Unix daemon process is tricky to get right, but the required steps are much the same for every daemon program. A DaemonContext instance holds the behaviour and configured process environment for the program; use the instance as a context manager to enter a daemon state.
py-python-gitlab¶
- Homepage:
- Spack package:
- Versions:
- 0.19, 0.18, 0.17, 0.16
- Build Dependencies:
- python, py-setuptools, py-requests, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-requests, py-six
- Description:
- Python wrapper for the GitLab API
py-pythonqwt¶
- Homepage:
- Spack package:
- Versions:
- 0.5.5
- Build Dependencies:
- py-numpy, py-sip, py-sphinx, py-pyqt, py-setuptools, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-sip, python, py-sphinx, py-pyqt
- Description:
- Qt plotting widgets for Python
py-pytz¶
- Homepage:
- Spack package:
- Versions:
- 2017.2, 2016.10, 2016.6.1, 2016.3, 2015.4, 2014.10, 2014.9
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- World timezone definitions, modern and historical.
py-pywavelets¶
- Homepage:
- Spack package:
- Versions:
- 0.5.2
- Build Dependencies:
- py-numpy, python, py-setuptools, py-cython
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- PyWavelets is a free Open Source library for wavelet transforms in Python
py-pyyaml¶
- Homepage:
- Spack package:
- Versions:
- 3.11
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- PyYAML is a YAML parser and emitter for Python.
py-qtawesome¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1, 0.3.3
- Build Dependencies:
- python, py-setuptools, py-qtpy, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-qtpy, py-six
- Description:
- FontAwesome icons in PyQt and PySide applications
py-qtconsole¶
- Homepage:
- Spack package:
- Versions:
- 4.2.1
- Build Dependencies:
- py-jupyter-core, py-sphinx, py-jupyter-client, py-setuptools, py-traitlets, python, py-pygments, py-ipykernel
- Link Dependencies:
- python
- Run Dependencies:
- py-jupyter-core, py-sphinx, py-jupyter-client, py-ipykernel, py-traitlets, python, py-pygments
- Description:
- Jupyter Qt console
py-qtpy¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- python, py-setuptools, py-pyqt
- Link Dependencies:
- python
- Run Dependencies:
- python, py-pyqt
- Description:
- QtPy: Abtraction layer for PyQt5/PyQt4/PySide
py-quantities¶
- Homepage:
- Spack package:
- Versions:
- 0.12.1, 0.11.1
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Support for physical quantities with units, based on numpy
py-radical-utils¶
- Homepage:
- Spack package:
- Versions:
- 0.45, 0.41.1
- Build Dependencies:
- python, py-netifaces, py-colorama, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-netifaces, py-colorama, python
- Description:
- Shared code and tools for various RADICAL Projects
py-ranger¶
- Homepage:
- Spack package:
- Versions:
- 1.7.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A VIM-inspired filemanager for the console
py-readme-renderer¶
- Homepage:
- Spack package:
- Versions:
- 16.0
- Build Dependencies:
- py-docutils, py-six, py-bleach, python, py-pygments, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-docutils, py-bleach, py-six, py-pygments
- Description:
- readme_renderer is a library for rendering "readme" descriptions for Warehouse.
py-regex¶
- Homepage:
- Spack package:
- Versions:
- 2017.07.11
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Alternative regular expression module, to replace re.
py-reportlab¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.
py-requests¶
- Homepage:
- Spack package:
- Versions:
- 2.14.2, 2.13.0, 2.11.1, 2.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python HTTP for Humans.
py-restview¶
- Homepage:
- Spack package:
- Versions:
- 2.6.1
- Build Dependencies:
- py-docutils, python, py-setuptools, py-pygments, py-readme-renderer
- Link Dependencies:
- python
- Run Dependencies:
- python, py-docutils, py-pygments, py-readme-renderer
- Description:
- A viewer for ReStructuredText documents that renders them on the fly.
py-rope¶
- Homepage:
- Spack package:
- Versions:
- 0.10.5
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- a python refactoring library.
py-rpy2¶
- Homepage:
- Spack package:
- Versions:
- 2.5.6, 2.5.4
- Build Dependencies:
- python, py-setuptools, py-six, r
- Link Dependencies:
- python, r
- Run Dependencies:
- python, py-six
- Description:
- rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.
py-rsa¶
- Homepage:
- Spack package:
- Versions:
- 3.4.2
- Build Dependencies:
- py-pyasn1, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-pyasn1, python, py-setuptools
- Description:
- Pure-Python RSA implementation
py-rseqc¶
- Homepage:
- Spack package:
- Versions:
- 2.6.4
- Build Dependencies:
- py-bx-python, py-numpy, r, py-pysam, py-setuptools, python
- Link Dependencies:
- python
- Run Dependencies:
- py-bx-python, py-numpy, python, py-pysam, r
- Description:
- RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA- seq data.
py-rtree¶
- Homepage:
- Spack package:
- Versions:
- 0.8.3
- Build Dependencies:
- python, py-setuptools, libspatialindex
- Link Dependencies:
- python, libspatialindex
- Run Dependencies:
- python
- Description:
- Python interface to the RTREE.4 Library.
py-saga-python¶
- Homepage:
- Spack package:
- Versions:
- 0.41.3
- Build Dependencies:
- python, py-setuptools, py-radical-utils, py-apache-libcloud
- Link Dependencies:
- python
- Run Dependencies:
- python, py-radical-utils, py-apache-libcloud
- Description:
- A light-weight access layer for distributed computing infrastructure
py-scandir¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- scandir, a better directory iterator and faster os.walk().
py-scientificpython¶
- Homepage:
- Spack package:
- Versions:
- 2.8.1
- Build Dependencies:
- py-numpy, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.
py-scikit-image¶
- Homepage:
- Spack package:
- Versions:
- 0.12.3
- Build Dependencies:
- python, pil, py-cython, py-scipy, py-networkx, py-matplotlib, py-setuptools, py-six, py-dask
- Link Dependencies:
- python
- Run Dependencies:
- python, py-scipy, py-networkx, py-matplotlib, pil, py-six, py-dask
- Description:
- Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.
py-scikit-learn¶
- Homepage:
- Spack package:
- Versions:
- 0.18.1, 0.17.1, 0.16.1, 0.15.2, 0.13.1
- Build Dependencies:
- py-numpy, python, py-scipy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- A set of python modules for machine learning and data mining.
py-scipy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0, 0.19.1, 0.19.0, 0.18.1, 0.17.0, 0.15.1, 0.15.0
- Build Dependencies:
- py-numpy, python, py-setuptools, lapack, blas
- Link Dependencies:
- lapack, python, blas
- Run Dependencies:
- py-numpy, python
- Description:
- SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.
py-seaborn¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1
- Build Dependencies:
- py-numpy, python, py-scipy, py-matplotlib, py-setuptools, py-pandas
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-matplotlib, python, py-pandas, py-scipy
- Description:
- Seaborn: statistical data visualization. Seaborn is a library for making attractive and informative statistical graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.
py-setuptools¶
- Homepage:
- Spack package:
- Versions:
- 35.0.2, 34.4.1, 34.2.0, 25.2.0, 20.7.0, 20.6.7, 20.5, 19.2, 18.1, 16.0, 11.3.1
- Build Dependencies:
- py-packaging, python, py-appdirs, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-packaging, python, py-appdirs, py-six
- Description:
- A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages.
py-setuptools-git¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- python, py-setuptools, git
- Link Dependencies:
- python, git
- Run Dependencies:
- python
- Description:
- Setuptools revision control system plugin for Git
py-setuptools-scm¶
- Homepage:
- Spack package:
- Versions:
- 1.15.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- the blessed package to manage your versions by scm tags
py-sfepy¶
- Homepage:
- Spack package:
- Versions:
- 2017.3
- Build Dependencies:
- py-numpy, py-setuptools, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, hdf5, py-pytables, py-scipy, py-petsc4py, py-matplotlib, python, py-six, py-sympy
- Description:
- SfePy (http://sfepy.org) is a software for solving systems of coupled partial differential equations (PDEs) by the finite element method in 1D, 2D and 3D. It can be viewed both as black-box PDE solver, and as a Python package which can be used for building custom applications.
py-sh¶
- Homepage:
- Spack package:
- Versions:
- 1.12.9, 1.11
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python subprocess interface
py-shiboken¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- python, py-sphinx, py-setuptools, qt, cmake, libxml2
- Link Dependencies:
- qt, python, libxml2
- Run Dependencies:
- python, py-sphinx
- Description:
- Shiboken generates bindings for C++ libraries using CPython.
py-simplegeneric¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1, 0.8
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Simple generic functions (similar to Python's own len(), pickle.dump(), etc.)
py-simplejson¶
- Homepage:
- Spack package:
- Versions:
- 3.10.0, 3.9.0, 3.8.2, 3.8.1, 3.8.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Simplejson is a simple, fast, extensible JSON encoder/decoder for Python
py-singledispatch¶
- Homepage:
- Spack package:
- Versions:
- 3.4.0.3
- Build Dependencies:
- python, py-setuptools, py-six
- Link Dependencies:
- python
- Run Dependencies:
- python, py-six
- Description:
- This library brings functools.singledispatch to Python 2.6-3.3.
py-sip¶
- Homepage:
- Spack package:
- Versions:
- 4.16.7, 4.16.5
- Build Dependencies:
- python
- Link Dependencies:
- python
- Description:
- SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
py-six¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0, 1.9.0, 1.8.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Python 2 and 3 compatibility utilities.
py-slepc4py¶
- Homepage:
- Spack package:
- Versions:
- 3.7.0
- Build Dependencies:
- python, py-petsc4py, py-setuptools, slepc
- Link Dependencies:
- slepc, python
- Run Dependencies:
- py-petsc4py, python
- Description:
- This package provides Python bindings for the SLEPc package.
py-sncosmo¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- py-numpy, py-astropy, py-iminuit, py-scipy, py-matplotlib, py-emcee, python, py-setuptools, py-nestle
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-astropy, py-iminuit, py-scipy, py-matplotlib, py-emcee, python, py-nestle
- Description:
- SNCosmo is a Python library for high-level supernova cosmology analysis.
py-snowballstemmer¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms.
py-spectra¶
- Homepage:
- Spack package:
- Versions:
- 0.0.8
- Build Dependencies:
- python, py-colormath, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-colormath, python
- Description:
- Color scales and color conversion made easy for Python.
py-spefile¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Reader for SPE files part of pyspec a set of python routines for data analysis of x-ray scattering experiments
py-spglib¶
- Homepage:
- Spack package:
- Versions:
- 1.9.9.18
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-setuptools
- Description:
- Python bindings for C library for finding and handling crystal symmetries.
py-sphinx¶
- Homepage:
- Spack package:
- Versions:
- 1.6.3, 1.6.1, 1.5.5, 1.4.5, 1.3.1
- Build Dependencies:
- py-alabaster, py-snowballstemmer, py-typing, py-sphinx-rtd-theme, py-setuptools, py-sphinxcontrib-websupport, py-babel, py-pygments, py-docutils, py-imagesize, py-jinja2, python, py-requests, py-six
- Link Dependencies:
- python
- Run Dependencies:
- py-alabaster, py-snowballstemmer, py-typing, py-sphinx-rtd-theme, py-setuptools, py-sphinxcontrib-websupport, py-babel, py-pygments, py-docutils, py-imagesize, py-jinja2, python, py-requests, py-six
- Description:
- Sphinx Documentation Generator.
py-sphinx-bootstrap-theme¶
- Homepage:
- Spack package:
- Versions:
- 0.4.13
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Sphinx Bootstrap Theme.
py-sphinx-rtd-theme¶
- Homepage:
- Spack package:
- Versions:
- 0.2.5b1, 0.1.10a0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- ReadTheDocs.org theme for Sphinx.
py-sphinxcontrib-bibtex¶
- Homepage:
- Spack package:
- Versions:
- 0.3.5
- Build Dependencies:
- py-pybtex, py-latexcodec, py-ordereddict, py-sphinx, py-six, py-setuptools, py-pybtex-docutils, python, py-oset
- Link Dependencies:
- python
- Run Dependencies:
- py-pybtex, py-latexcodec, py-ordereddict, py-sphinx, py-six, py-pybtex-docutils, python, py-oset
- Description:
- A Sphinx extension for BibTeX style citations.
py-sphinxcontrib-programoutput¶
- Homepage:
- Spack package:
- Versions:
- 0.10
- Build Dependencies:
- python, py-setuptools, py-sphinx
- Link Dependencies:
- python
- Run Dependencies:
- python, py-sphinx
- Description:
- A Sphinx extension to literally insert the output of arbitrary commands into documents, helping you to keep your command examples up to date.
py-sphinxcontrib-websupport¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- sphinxcontrib-webuspport provides a Python API to easily integrate Sphinx documentation into your Web application.
py-spyder¶
- Homepage:
- Spack package:
- Versions:
- 3.1.3, 2.3.9
- Build Dependencies:
- py-numpydoc, py-qtpy, py-setuptools, py-rope, py-pickleshare, py-zmq, py-chardet, py-nbconvert, py-pyflakes, py-qtawesome, py-sphinx, py-pycodestyle, py-pylint, python, py-jedi, py-psutil, py-pygments, py-qtconsole
- Link Dependencies:
- python
- Run Dependencies:
- py-numpydoc, py-qtpy, python, py-rope, py-pickleshare, py-zmq, py-chardet, py-nbconvert, py-pyflakes, py-qtawesome, py-sphinx, py-pycodestyle, py-pylint, py-jedi, py-psutil, py-pygments, py-qtconsole
- Description:
- Scientific PYthon Development EnviRonment
py-spykeutils¶
- Homepage:
- Spack package:
- Versions:
- 0.4.3
- Build Dependencies:
- python, py-setuptools, py-scipy, py-quantities, py-neo
- Link Dependencies:
- python
- Run Dependencies:
- py-neo, python, py-scipy, py-quantities
- Description:
- Utilities for analyzing electrophysiological data
py-sqlalchemy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.12
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The Python SQL Toolkit and Object Relational Mapper
py-statsmodels¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0
- Build Dependencies:
- py-numpy, py-cython, py-scipy, py-patsy, py-setuptools, python, py-pandas
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-cython, py-scipy, py-patsy, py-matplotlib, python, py-pandas
- Description:
- Statistical computations and models for use with SciPy
py-storm¶
- Homepage:
- Spack package:
- Versions:
- 0.20
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Storm is an object-relational mapper (ORM) for Python
py-subprocess32¶
- Homepage:
- Spack package:
- Versions:
- 3.2.7
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A backport of the subprocess module from Python 3.2/3.3 for 2.x.
py-symengine¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.2.0
- Build Dependencies:
- python, py-setuptools, py-cython, symengine, cmake
- Link Dependencies:
- python, symengine
- Run Dependencies:
- python
- Description:
- Python wrappers for SymEngine, a symbolic manipulation library.
py-symfit¶
- Homepage:
- Spack package:
- Versions:
- 0.3.5
- Build Dependencies:
- py-setuptools, py-pbr, python
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-funcsigs, python, py-scipy, py-sympy
- Description:
- Symbolic Fitting; fitting as it should be.
py-sympy¶
- Homepage:
- Spack package:
- Versions:
- 1.0, 0.7.6
- Build Dependencies:
- py-mpmath, python
- Link Dependencies:
- python
- Run Dependencies:
- py-mpmath, python
- Description:
- SymPy is a Python library for symbolic mathematics.
py-tabulate¶
- Homepage:
- Spack package:
- Versions:
- 0.7.7
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Pretty-print tabular data
py-tappy¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Build Dependencies:
- py-nose, python, py-pygments, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-nose, python, py-pygments
- Description:
- Python TAP interface module for unit tests
py-terminado¶
- Homepage:
- Spack package:
- Versions:
- 0.6
- Build Dependencies:
- py-ptyprocess, python, py-tornado
- Link Dependencies:
- python
- Run Dependencies:
- py-ptyprocess, python, py-tornado
- Description:
- Terminals served to term.js using Tornado websockets
py-tetoolkit¶
- Homepage:
- Spack package:
- Versions:
- 1.5.1
- Build Dependencies:
- py-pysam, python, py-setuptools, r-deseq
- Link Dependencies:
- python, py-setuptools
- Run Dependencies:
- py-pysam, python, r-deseq
- Description:
- TEToolkit is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments.
py-theano¶
- Homepage:
- Spack package:
- Versions:
- 0.8.2, master
- Build Dependencies:
- py-numpy, cuda, libgpuarray, py-scipy, py-setuptools, python, py-six, blas
- Link Dependencies:
- cuda, libgpuarray, python, blas
- Run Dependencies:
- py-numpy, py-setuptools, python, py-six, py-scipy
- Description:
- Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.
py-tifffile¶
- Homepage:
- Spack package:
- Versions:
- 0.12.1
- Build Dependencies:
- py-numpy, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python
- Description:
- Read and write image data from and to TIFF files.
py-toml¶
- Homepage:
- Spack package:
- Versions:
- 0.9.3
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Python library for parsing and creating TOML configuration files. For more information on the TOML standard, see https://github.com/toml- lang/toml.git
py-tomopy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- py-numpy, py-dxchange, py-h5py, py-scipy, py-scikit-image, py-setuptools, py-pywavelets, python, py-six, py-pyfftw
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-dxchange, py-h5py, py-scipy, py-scikit-image, py-pyfftw, py-pywavelets, python, py-six
- Description:
- TomoPy is an open-source Python package for tomographic data processing and image reconstruction.
py-tornado¶
- Homepage:
- Spack package:
- Versions:
- 4.4.0
- Build Dependencies:
- py-singledispatch, py-backports-ssl-match-hostname, python, py-backports-abc, py-setuptools, py-certifi
- Link Dependencies:
- python
- Run Dependencies:
- py-singledispatch, py-backports-abc, python, py-certifi, py-backports-ssl-match-hostname
- Description:
- Tornado is a Python web framework and asynchronous networking library.
py-tqdm¶
- Homepage:
- Spack package:
- Versions:
- 4.8.4
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A Fast, Extensible Progress Meter
py-traceback2¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- python, py-pbr, py-setuptools, py-linecache2
- Link Dependencies:
- python
- Run Dependencies:
- py-pbr, python, py-linecache2
- Description:
- Backports of the traceback module
py-traitlets¶
- Homepage:
- Spack package:
- Versions:
- 4.3.1, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.0, 4.0.0, 4.0
- Build Dependencies:
- py-ipython-genutils, py-decorator, python, py-enum34
- Link Dependencies:
- python
- Run Dependencies:
- py-ipython-genutils, py-decorator, python, py-enum34
- Description:
- Traitlets Python config system
py-tuiview¶
- Homepage:
- Spack package:
- Versions:
- 1.1.7
- Build Dependencies:
- py-numpy, gdal, python, py-pyqt
- Link Dependencies:
- gdal, python
- Run Dependencies:
- py-numpy, python, py-pyqt
- Description:
- TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.
py-twisted¶
- Homepage:
- Spack package:
- Versions:
- 15.4.0, 15.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- An asynchronous networking framework written in Python
py-typing¶
- Homepage:
- Spack package:
- Versions:
- 3.6.1
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- This is a backport of the standard library typing module to Python versions older than 3.6.
py-tzlocal¶
- Homepage:
- Spack package:
- Versions:
- 1.3
- Build Dependencies:
- py-pytz, python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- py-pytz, python
- Description:
- tzinfo object for the local timezone.
py-umi-tools¶
- Homepage:
- Spack package:
- Versions:
- 0.5.3
- Build Dependencies:
- py-numpy, py-setuptools, py-pandas, py-scipy, py-regex, py-pysam, py-matplotlib, python, py-six, py-future
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-pandas, py-scipy, py-regex, py-pysam, py-matplotlib, python, py-six, py-future
- Description:
- Tools for handling Unique Molecular Identifiers in NGS data sets
py-unittest2¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- python, py-enum34, py-setuptools, py-argparse, py-six, py-traceback2
- Link Dependencies:
- python
- Run Dependencies:
- py-enum34, python, py-argparse, py-six, py-traceback2
- Description:
- unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 and onwards.
py-unittest2py3k¶
- Homepage:
- Spack package:
- Versions:
- 0.5.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 and 3.2. This is a Python 3 compatible version of unittest2.
py-urllib3¶
- Homepage:
- Spack package:
- Versions:
- 1.20, 1.14
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- HTTP library with thread-safe connection pooling, file post, and more.
py-urwid¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A full-featured console UI library
py-vcversioner¶
- Homepage:
- Spack package:
- Versions:
- 2.16.0.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Vcversioner: Take version numbers from version control.
py-virtualenv¶
- Homepage:
- Spack package:
- Versions:
- 15.1.0, 15.0.1, 13.0.1, 1.11.6
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- virtualenv is a tool to create isolated Python environments.
py-vsc-base¶
- Homepage:
- Spack package:
- Versions:
- 2.5.8
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- Common Python libraries tools created by HPC-UGent
py-vsc-install¶
- Homepage:
- Spack package:
- Versions:
- 0.10.25
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python, py-setuptools
- Description:
- Shared setuptools functions and classes for Python libraries developed by HPC-UGent.
py-wcsaxes¶
- Homepage:
- Spack package:
- Versions:
- 0.8
- Build Dependencies:
- py-numpy, py-astropy, python, py-setuptools, py-matplotlib
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-astropy, python, py-matplotlib
- Description:
- WCSAxes is a framework for making plots of Astronomical data in Matplotlib.
py-wcwidth¶
- Homepage:
- Spack package:
- Versions:
- 0.1.7
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Measures number of Terminal column cells of wide-character codes
py-webkit-server¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- a Webkit-based, headless web client
py-werkzeug¶
- Homepage:
- Spack package:
- Versions:
- 0.11.15, 0.11.11
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- The Swiss Army knife of Python web development
py-wheel¶
- Homepage:
- Spack package:
- Versions:
- 0.29.0, 0.26.0
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A built-package format for Python.
py-widgetsnbextension¶
- Homepage:
- Spack package:
- Versions:
- 1.2.6
- Build Dependencies:
- python, py-setuptools, py-jupyter-notebook
- Link Dependencies:
- python
- Run Dependencies:
- python, py-jupyter-notebook
- Description:
- IPython HTML widgets for Jupyter
py-wrapt¶
- Homepage:
- Spack package:
- Versions:
- 1.10.10
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Module for decorators, wrappers and monkey patching.
py-xarray¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1
- Build Dependencies:
- py-numpy, python, py-setuptools, py-pandas
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, python, py-pandas
- Description:
- N-D labeled arrays and datasets in Python
py-xattr¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- A python interface to access extended file attributes, sans libattr dependency
py-xlrd¶
- Homepage:
- Spack package:
- Versions:
- 0.9.4
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Library for developers to extract data from Microsoft Excel (tm) spreadsheet files
py-xlsxwriter¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- XlsxWriter is a Python module for writing files in the Excel 2007+ XLSX file format.
py-xmlrunner¶
- Homepage:
- Spack package:
- Versions:
- 1.7.7
- Build Dependencies:
- python, py-setuptools, py-unittest2
- Link Dependencies:
- python
- Run Dependencies:
- python, py-unittest2
- Description:
- PyUnit-based test runner with JUnit like XML reporting.
py-xopen¶
- Homepage:
- Spack package:
- Versions:
- 0.1.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- This small Python module provides a xopen function that works like the built-in open function, but can also deal with compressed files. Supported compression formats are gzip, bzip2 and xz. They are automatically recognized by their file extensions .gz, .bz2 or .xz.
py-xpyb¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- xcb-proto, python, libxcb
- Link Dependencies:
- python, libxcb
- Description:
- xpyb provides a Python binding to the X Window System protocol via libxcb.
py-xvfbwrapper¶
- Homepage:
- Spack package:
- Versions:
- 0.2.9
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- run headless display inside X virtual framebuffer (Xvfb)
py-yapf¶
- Homepage:
- Spack package:
- Versions:
- 0.2.1
- Build Dependencies:
- python, py-setuptools
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- Yet Another Python Formatter
py-yt¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.4.0, 3.3.5, 3.3.4, 3.3.1, 3.2.3, 3.1.0, 3.0.2, 2.6.3
- Build Dependencies:
- py-numpy, py-astropy, py-ipython, py-cython, py-scipy, py-matplotlib, python, py-h5py, rockstar, py-setuptools, py-sympy
- Link Dependencies:
- python
- Run Dependencies:
- py-numpy, py-astropy, py-ipython, py-cython, py-scipy, py-matplotlib, python, py-h5py, rockstar, py-setuptools, py-sympy
- Description:
- Volumetric Data Analysis yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
py-zmq¶
- Homepage:
- Spack package:
- Versions:
- 16.0.2, 14.7.0
- Build Dependencies:
- py-cffi, zeromq, python, py-cython, py-py
- Link Dependencies:
- zeromq, python
- Run Dependencies:
- py-cffi, python, py-cython, py-py
- Description:
- PyZMQ: Python bindings for zeromq.
python¶
- Homepage:
- Spack package:
- Versions:
- 3.6.3, 3.6.2, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.3.6, 3.2.6, 3.1.5, 2.7.14, 2.7.13, 2.7.12, 2.7.11, 2.7.10, 2.7.9, 2.7.8
- Build Dependencies:
- ncurses, openssl, sqlite, bzip2, tk, tcl, zlib, readline
- Link Dependencies:
- ncurses, openssl, sqlite, bzip2, tk, tcl, zlib, readline
- Description:
- The Python programming language.
qbank¶
- Homepage:
- Spack package:
- Versions:
- 2.10.4
- Build Dependencies:
- openssl, perl, perl-dbi
- Link Dependencies:
- openssl
- Run Dependencies:
- perl, perl-dbi
- Description:
- QBank is a unique dynamic reservation-based allocation management system that manages the utilization of computational resources in a multi- project environment. It is used in conjunction with a resource management system allowing an organization to guarantee greater fairness and enforce mission priorities by associating a charge with the use of computational resources and allocating resource credits which limit how much of the resources may be used at what time and by whom. It tracks resource utilization and allows for insightful planning.
qbox¶
- Homepage:
- Spack package:
- Versions:
- 1.63.7, 1.63.5, 1.63.4, 1.63.2, 1.63.0, 1.62.3, 1.60.9, 1.60.4, 1.60.0, 1.58.0, 1.56.2, 1.54.4, 1.54.2, 1.52.3, 1.52.2, 1.50.4, 1.50.2, 1.50.1, 1.47.0, 1.45.3, 1.45.1, 1.45.0, 1.44.0
- Build Dependencies:
- scalapack, fftw, mpi, xerces-c, blas
- Link Dependencies:
- scalapack, fftw, mpi, xerces-c, blas
- Description:
- Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.
qhull¶
- Homepage:
- Spack package:
- Versions:
- 2015.2, 2012.1
- Build Dependencies:
- cmake
- Description:
- Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.
qmcpack¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.3.0, 3.2.0, 3.1.1, 3.1.0
- Build Dependencies:
- cuda, fftw, hdf5, espresso, boost, mpi, lapack, blas, cmake, libxml2
- Link Dependencies:
- cuda, fftw, espresso, boost, mpi, lapack, blas, hdf5, libxml2
- Run Dependencies:
- py-numpy, py-matplotlib
- Description:
- QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code.
qmd-progress¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0.0
- Build Dependencies:
- cmake, metis, bml, mpi
- Link Dependencies:
- metis, bml, mpi
- Description:
- PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver. This library is focused on the development of general solvers that are commonly used in quantum chemistry packages.
qrupdate¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- lapack, blas
- Link Dependencies:
- lapack, blas
- Description:
- qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
qt¶
- Homepage:
- Spack package:
- Versions:
- 5.10.0, 5.9.1, 5.9.0, 5.8.0, 5.7.1, 5.7.0, 5.5.1, 5.4.2, 5.4.0, 5.3.2, 5.2.1, 4.8.6, 3.3.8b
- Build Dependencies:
- libpng, zlib, icu4c, flex, gl, gperf, bison, jpeg, glib, libxext, gtkplus, fontconfig, freetype, libx11, dbus, libmng, openssl, libtiff, python, libxcb, libxml2
- Link Dependencies:
- libpng, zlib, icu4c, fontconfig, gl, gperf, jpeg, glib, libxext, gtkplus, freetype, libx11, dbus, libmng, openssl, libtiff, libxcb, libxml2
- Description:
- Qt is a comprehensive cross-platform C++ application framework.
qt-creator¶
- Homepage:
- Spack package:
- Versions:
- 4.4.0, 4.3.1, 4.1.0
- Build Dependencies:
- qt, sqlite
- Link Dependencies:
- qt, sqlite
- Description:
- The Qt Creator IDE.
qtgraph¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- qt, graphviz
- Link Dependencies:
- qt, graphviz
- Description:
- The baseline library used in the CUDA-centric Open|SpeedShop Graphical User Interface (GUI) which allows Graphviz DOT formatted data to be imported into a Qt application by wrapping the Graphviz libcgraph and libgvc within the Qt Graphics View Framework.
qthreads¶
- Homepage:
- Spack package:
- Versions:
- 1.12, 1.11, 1.10
- Build Dependencies:
- hwloc
- Link Dependencies:
- hwloc
- Description:
- The qthreads API is designed to make using large numbers of threads convenient and easy, and to allow portable access to threading constructs used in massively parallel shared memory environments. The API maps well to both MTA-style threading and PIM-style threading, and we provide an implementation of this interface in both a standard SMP context as well as the SST context. The qthreads API provides access to full/empty-bit (FEB) semantics, where every word of memory can be marked either full or empty, and a thread can wait for any word to attain either state.
quinoa¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- hypre, hdf5, pugixml, random123, pegtl, mad-numdiff, cmake, h5part, trilinos, boost, tut, pstreams, netlib-lapack, boostmplcartesianproduct, charm
- Link Dependencies:
- hypre, hdf5, pugixml, random123, pegtl, mad-numdiff, h5part, trilinos, boost, tut, pstreams, netlib-lapack, boostmplcartesianproduct, charm
- Description:
- Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it is a test-bed to experiment with various algorithms using fully asynchronous runtime systems.
qwt¶
- Homepage:
- Spack package:
- Versions:
- 6.1.3, 5.2.2
- Build Dependencies:
- qt
- Link Dependencies:
- qt
- Description:
- The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.
r¶
- Homepage:
- Spack package:
- Versions:
- 3.4.3, 3.4.2, 3.4.1, 3.4.0, 3.3.3, 3.3.2, 3.3.1, 3.3.0, 3.2.3, 3.2.2, 3.2.1, 3.2.0, 3.1.3, 3.1.2
- Build Dependencies:
- blas, zlib, libxt, lapack, tcl, bzip2, curl, pcre, jpeg, glib, ncurses, freetype, libx11, icu4c, pango, tk, java, libtiff, readline, cairo
- Link Dependencies:
- blas, zlib, libxt, lapack, tcl, bzip2, curl, pcre, jpeg, glib, ncurses, freetype, libx11, icu4c, pango, tk, java, libtiff, readline, cairo
- Description:
- R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.
r-a4¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-a4preproc, r-a4reporting, r-a4base, r-a4core, r, r-a4classif
- Link Dependencies:
- r
- Run Dependencies:
- r-a4preproc, r-a4reporting, r-a4base, r-a4core, r, r-a4classif
- Description:
- Automated Affymetrix Array Analysis Umbrella Package.
r-a4base¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-glmnet, r-genefilter, r-biobase, r-multtest, r, r-annotationdbi, r-gplots, r-mpm, r-annaffy, r-a4preproc, r-limma, r-a4core
- Link Dependencies:
- r
- Run Dependencies:
- r-glmnet, r-genefilter, r-biobase, r-multtest, r, r-annotationdbi, r-gplots, r-mpm, r-annaffy, r-a4preproc, r-limma, r-a4core
- Description:
- Automated Affymetrix Array Analysis.
r-a4classif¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-pamr, r-mlinterfaces, r-a4preproc, r-varselrf, r, r-a4core, r-glmnet, r-rocr
- Link Dependencies:
- r
- Run Dependencies:
- r-pamr, r-mlinterfaces, r-a4preproc, r-varselrf, r, r-a4core, r-glmnet, r-rocr
- Description:
- Automated Affymetrix Array Analysis Classification Package.
r-a4core¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-biobase, r-glmnet, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-glmnet, r
- Description:
- Automated Affymetrix Array Analysis Core Package.
r-a4preproc¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- Automated Affymetrix Array Analysis Preprocessing Package.
r-a4reporting¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-xtable, r-annaffy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-xtable, r-annaffy, r
- Description:
- Automated Affymetrix Array Analysis Reporting Package.
r-abadata¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes.
r-abaenrichment¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- r-gplots, r, r-rcpp, r-abadata, r-gtools
- Link Dependencies:
- r
- Run Dependencies:
- r-gplots, r, r-rcpp, r-abadata, r-gtools
- Description:
- The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like 'get_expression' and 'plot_expression' facilitate exploring the expression data. From version 1.3.5 onwards genomic regions can be provided as input, too; and from version 1.5.9 onwards the function 'get_annotated_genes' offers an easy way to obtain annotations of genes to enriched or user-defined brain regions.
r-abind¶
- Homepage:
- Spack package:
- Versions:
- 1.4-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.
r-absseq¶
- Homepage:
- Spack package:
- Versions:
- 1.22.8
- Build Dependencies:
- r-locfit, r-limma, r
- Link Dependencies:
- r
- Run Dependencies:
- r-locfit, r-limma, r
- Description:
- Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.
r-acde¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- r-boot, r
- Link Dependencies:
- r
- Run Dependencies:
- r-boot, r
- Description:
- This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).
r-acepack¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- ACE and AVAS for Selecting Multiple Regression Transformations.
r-acgh¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-multtest, r, r-survival, r-cluster, r-biobase
- Link Dependencies:
- r
- Run Dependencies:
- r-multtest, r, r-survival, r-cluster, r-biobase
- Description:
- Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
r-acme¶
- Homepage:
- Spack package:
- Versions:
- 2.32.0
- Build Dependencies:
- r-biobase, r, r-biocgenerics
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r, r-biocgenerics
- Description:
- ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.
r-ada¶
- Homepage:
- Spack package:
- Versions:
- 2.0-5
- Build Dependencies:
- r-rpart, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rpart, r
- Description:
- Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.
r-adabag¶
- Homepage:
- Spack package:
- Versions:
- 4.1
- Build Dependencies:
- r-caret, r-rpart, r-mlbench, r
- Link Dependencies:
- r
- Run Dependencies:
- r-caret, r-rpart, r-mlbench, r
- Description:
- Applies Multiclass AdaBoost.M1, SAMME and Bagging.
r-ade4¶
- Homepage:
- Spack package:
- Versions:
- 1.7-6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
r-adegenet¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- r-seqinr, r-ggplot2, r-reshape2, r-ape, r-spdep, r, r-igraph, r-ade4, r-shiny, r-dplyr, r-vegan
- Link Dependencies:
- r
- Run Dependencies:
- r-seqinr, r-ggplot2, r-reshape2, r-ape, r-spdep, r, r-igraph, r-ade4, r-shiny, r-dplyr, r-vegan
- Description:
- Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
r-adsplit¶
- Homepage:
- Spack package:
- Versions:
- 1.46.0
- Build Dependencies:
- r-biobase, r-kegg-db, r-cluster, r, r-go-db, r-annotationdbi, r-multtest
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-kegg-db, r-cluster, r, r-go-db, r-annotationdbi, r-multtest
- Description:
- This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
r-affxparser¶
- Homepage:
- Spack package:
- Versions:
- 1.48.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
r-affy¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-biocgenerics, r-biobase, r-biocinstaller, r, r-preprocesscore, r-affyio, r-zlibbioc
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-biobase, r-biocinstaller, r, r-preprocesscore, r-affyio, r-zlibbioc
- Description:
- The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
r-affycomp¶
- Homepage:
- Spack package:
- Versions:
- 1.52.0
- Build Dependencies:
- r-biobase, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r
- Description:
- The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
r-affycompatible¶
- Homepage:
- Spack package:
- Versions:
- 1.36.0
- Build Dependencies:
- r-biostrings, r-xml, r-rcurl, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biostrings, r-xml, r-rcurl, r
- Description:
- This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.
r-affycontam¶
- Homepage:
- Spack package:
- Versions:
- 1.34.0
- Build Dependencies:
- r-biobase, r-affydata, r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-affydata, r-affy, r
- Description:
- structured corruption of cel file data to demonstrate QA effectiveness.
r-affycoretools¶
- Homepage:
- Spack package:
- Versions:
- 1.48.0
- Build Dependencies:
- r-rsqlite, r-ggplot2, r-affy, r, r-gcrma, r-gostats, r-biocgenerics, r-hwriter, r-annotationdbi, r-reportingtools, r-gplots, r-biobase, r-limma, r-xtable, r-edger, r-s4vectors, r-oligoclasses, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-ggplot2, r-affy, r, r-gcrma, r-gostats, r-biocgenerics, r-hwriter, r-annotationdbi, r-reportingtools, r-gplots, r-biobase, r-limma, r-xtable, r-edger, r-s4vectors, r-oligoclasses, r-lattice
- Description:
- Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.
r-affydata¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-affy, r
- Description:
- Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy.
r-affyexpress¶
- Homepage:
- Spack package:
- Versions:
- 1.42.0
- Build Dependencies:
- r-affy, r-limma, r
- Link Dependencies:
- r
- Run Dependencies:
- r-affy, r-limma, r
- Description:
- The purpose of this package is to provide a comprehensive and easy-to- use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
r-affyilm¶
- Homepage:
- Spack package:
- Versions:
- 1.28.0
- Build Dependencies:
- r-gcrma, r-biobase, r-affxparser, r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gcrma, r-biobase, r-affxparser, r-affy, r
- Description:
- affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.
r-affyio¶
- Homepage:
- Spack package:
- Versions:
- 1.46.0
- Build Dependencies:
- r-zlibbioc, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zlibbioc, r
- Description:
- Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
r-affypdnn¶
- Homepage:
- Spack package:
- Versions:
- 1.50.0
- Build Dependencies:
- r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-affy, r
- Description:
- The package contains functions to perform the PDNN method described by Li Zhang et al.
r-affyplm¶
- Homepage:
- Spack package:
- Versions:
- 1.52.1
- Build Dependencies:
- r-biocgenerics, r-affy, r-zlibbioc, r-biobase, r-gcrma, r, r-preprocesscore
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-affy, r-zlibbioc, r-biobase, r-gcrma, r, r-preprocesscore
- Description:
- A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
r-affyqcreport¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-biobase, r-xtable, r-affy, r-simpleaffy, r-affyplm, r-genefilter, r, r-rcolorbrewer, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-xtable, r-affy, r-simpleaffy, r-affyplm, r-genefilter, r, r-rcolorbrewer, r-lattice
- Description:
- This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
r-affyrnadegradation¶
- Homepage:
- Spack package:
- Versions:
- 1.22.0
- Build Dependencies:
- r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-affy, r
- Description:
- The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
r-agdex¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-biobase, r, r-gseabase
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r, r-gseabase
- Description:
- A tool to evaluate agreement of differential expression for cross- species genomics.
r-agilp¶
- Homepage:
- Spack package:
- Versions:
- 3.8.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Agilent expression array processing package.
r-agimicrorna¶
- Homepage:
- Spack package:
- Versions:
- 2.26.0
- Build Dependencies:
- r-biobase, r-affy, r, r-preprocesscore, r-limma, r-affycoretools
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-affy, r, r-preprocesscore, r-limma, r-affycoretools
- Description:
- Processing and Analysis of Agilent microRNA data.
r-aims¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- r-e1071, r, r-biobase
- Link Dependencies:
- r
- Run Dependencies:
- r-e1071, r, r-biobase
- Description:
- This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.
r-aldex2¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- r-summarizedexperiment, r-genomicranges, r, r-s4vectors, r-iranges, r-biocparallel
- Link Dependencies:
- r
- Run Dependencies:
- r-summarizedexperiment, r-genomicranges, r, r-s4vectors, r-iranges, r-biocparallel
- Description:
- A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high- throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.
r-allelicimbalance¶
- Homepage:
- Spack package:
- Versions:
- 1.14.0
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r-genomeinfodb, r-genomicfeatures, r-seqinr, r, r-nlme, r-annotationdbi, r-variantannotation, r-rsamtools, r-iranges, r-summarizedexperiment, r-latticeextra, r-genomicranges, r-gridextra, r-s4vectors, r-gviz, r-bsgenome, r-biostrings, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r-genomeinfodb, r-genomicfeatures, r-seqinr, r, r-nlme, r-annotationdbi, r-variantannotation, r-rsamtools, r-iranges, r-summarizedexperiment, r-latticeextra, r-genomicranges, r-gridextra, r-s4vectors, r-gviz, r-bsgenome, r-biostrings, r-lattice
- Description:
- Provides a framework for allelic specific expression investigation using RNA-seq data.
r-alpine¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r-genomicalignments, r-speedglm, r-genomeinfodb, r, r-rbgl, r-rsamtools, r-iranges, r-graph, r-biostrings, r-genomicranges, r-genomicfeatures, r-s4vectors, r-summarizedexperiment, r-stringr
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-speedglm, r-genomeinfodb, r, r-rbgl, r-rsamtools, r-iranges, r-graph, r-biostrings, r-genomicranges, r-genomicfeatures, r-s4vectors, r-summarizedexperiment, r-stringr
- Description:
- Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.
r-als¶
- Homepage:
- Spack package:
- Versions:
- 0.0.6
- Build Dependencies:
- r-nnls, r-iso, r
- Link Dependencies:
- r
- Run Dependencies:
- r-nnls, r-iso, r
- Description:
- Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.
r-alsace¶
- Homepage:
- Spack package:
- Versions:
- 1.12.0
- Build Dependencies:
- r-als, r-ptw, r
- Link Dependencies:
- r
- Run Dependencies:
- r-als, r-ptw, r
- Description:
- Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.
r-altcdfenvs¶
- Homepage:
- Spack package:
- Versions:
- 2.38.0
- Build Dependencies:
- r-biocgenerics, r-makecdfenv, r-affy, r-biobase, r-s4vectors, r, r-hypergraph, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-makecdfenv, r-affy, r-biobase, r-s4vectors, r, r-hypergraph, r-biostrings
- Description:
- Convenience data structures and functions to handle cdfenvs.
r-ampliqueso¶
- Homepage:
- Spack package:
- Versions:
- 1.14.0
- Build Dependencies:
- r-ggplot2, r-doparallel, r-genefilter, r, r-edger, r-statmod, r-foreach, r-knitr, r-samr, r-deseq, r-gplots, r-xtable, r-rnaseqmap, r-rgl, r-variantannotation
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-doparallel, r-genefilter, r, r-edger, r-statmod, r-foreach, r-knitr, r-samr, r-deseq, r-gplots, r-xtable, r-rnaseqmap, r-rgl, r-variantannotation
- Description:
- The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq.
r-analysispageserver¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0
- Build Dependencies:
- r-biobase, r-log4r, r-rjson, r-graph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-log4r, r-rjson, r-graph, r
- Description:
- AnalysisPageServer is a modular system that enables sharing of customizable R analyses via the web.
r-anaquin¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r-qvalue, r-ggplot2, r-locfit, r, r-plyr, r-deseq2, r-knitr, r-rocr
- Link Dependencies:
- r
- Run Dependencies:
- r-qvalue, r-ggplot2, r-locfit, r, r-plyr, r-deseq2, r-knitr, r-rocr
- Description:
- The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.
r-aneufinder¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r-doparallel, r-rsamtools, r-ggplot2, r-genomeinfodb, r-bamsignals, r, r-iranges, r-reshape2, r-mclust, r-cowplot, r-foreach, r-genomicranges, r-ggrepel, r-ggdendro, r-s4vectors, r-aneufinderdata, r-biostrings, r-dnacopy, r-reordercluster
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r-doparallel, r-rsamtools, r-ggplot2, r-genomeinfodb, r-bamsignals, r, r-iranges, r-reshape2, r-mclust, r-cowplot, r-foreach, r-genomicranges, r-ggrepel, r-ggdendro, r-s4vectors, r-aneufinderdata, r-biostrings, r-dnacopy, r-reordercluster
- Description:
- This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.
r-aneufinderdata¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.
r-annaffy¶
- Homepage:
- Spack package:
- Versions:
- 1.48.0
- Build Dependencies:
- r-biobase, r-go-db, r-kegg-db, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-go-db, r-kegg-db, r
- Description:
- Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.
r-annotate¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-xtable, r-annotationdbi, r-xml, r-rcurl, r
- Link Dependencies:
- r
- Run Dependencies:
- r-xtable, r-annotationdbi, r-xml, r-rcurl, r
- Description:
- Using R enviroments for annotation.
r-annotationdbi¶
- Homepage:
- Spack package:
- Versions:
- 1.38.2
- Build Dependencies:
- r-rsqlite, r-biocgenerics, r-biobase, r-dbi, r, r-iranges
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-biocgenerics, r-biobase, r-dbi, r, r-iranges
- Description:
- Provides user interface and database connection code for annotation data packages using SQLite data storage.
r-annotationfilter¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r, r-genomicranges, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r, r-genomicranges, r-lazyeval
- Description:
- This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.
r-annotationforge¶
- Homepage:
- Spack package:
- Versions:
- 1.18.2
- Build Dependencies:
- r-rsqlite, r-biocgenerics, r-dbi, r-xml, r-biobase, r-s4vectors, r, r-annotationdbi, r-rcurl
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-biocgenerics, r-dbi, r-xml, r-biobase, r-s4vectors, r, r-annotationdbi, r-rcurl
- Description:
- Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.
r-annotationhub¶
- Homepage:
- Spack package:
- Versions:
- 2.8.3
- Build Dependencies:
- r-rsqlite, r-httr, r-interactivedisplaybase, r-yaml, r, r-s4vectors, r-annotationdbi, r-biocinstaller
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-httr, r-interactivedisplaybase, r-yaml, r, r-s4vectors, r-annotationdbi, r-biocinstaller
- Description:
- This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
r-ape¶
- Homepage:
- Spack package:
- Versions:
- 4.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non- contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
r-assertthat¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0, 0.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.
r-backports¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1, 1.1.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.
r-bamsignals¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- r-rhtslib, r-biocgenerics, r-genomicranges, r, r-iranges, r-rcpp, r-zlibbioc
- Link Dependencies:
- r
- Run Dependencies:
- r-rhtslib, r-biocgenerics, r-genomicranges, r, r-iranges, r-rcpp, r-zlibbioc
- Description:
- This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired- end data.
r-base64¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- r-openssl, r
- Link Dependencies:
- r
- Run Dependencies:
- r-openssl, r
- Description:
- Compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the 'openssl' or 'base64enc' package instead.
r-base64enc¶
- Homepage:
- Spack package:
- Versions:
- 0.1-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.
r-beanplot¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.
r-bh¶
- Homepage:
- Spack package:
- Versions:
- 1.65.0-1, 1.60.0-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.60.0-2, the following Boost libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' 'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset' 'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric' 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.
r-bindr¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides a simple interface for creating active bindings where the bound function accepts additional arguments.
r-bindrcpp¶
- Homepage:
- Spack package:
- Versions:
- 0.2
- Build Dependencies:
- r-bindr, r-plogr, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-bindr, r-plogr, r-rcpp, r
- Description:
- Provides an easy way to fill an environment with active bindings that call a C++ function.
r-biobase¶
- Homepage:
- Spack package:
- Versions:
- 2.36.2
- Build Dependencies:
- r-biocgenerics, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r
- Description:
- Functions that are needed by many other packages or which replace R functions.
r-biocgenerics¶
- Homepage:
- Spack package:
- Versions:
- 0.22.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- S4 generic functions needed by many Bioconductor packages.
r-biocinstaller¶
- Homepage:
- Spack package:
- Versions:
- 1.26.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package is used to install and update Bioconductor, CRAN, and (some) github packages.
r-biocparallel¶
- Homepage:
- Spack package:
- Versions:
- 1.10.1
- Build Dependencies:
- r-futile-logger, r-snow, r
- Link Dependencies:
- r
- Run Dependencies:
- r-futile-logger, r-snow, r
- Description:
- This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
r-biocstyle¶
- Homepage:
- Spack package:
- Versions:
- 2.4.1
- Build Dependencies:
- r-bookdown, r, r-knitr, r-yaml, r-rmarkdown
- Link Dependencies:
- r
- Run Dependencies:
- r-bookdown, r, r-knitr, r-yaml, r-rmarkdown
- Description:
- Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.
r-biomart¶
- Homepage:
- Spack package:
- Versions:
- 2.32.1
- Build Dependencies:
- r-annotationdbi, r-xml, r-rcurl, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r-xml, r-rcurl, r
- Description:
- In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.
r-biomformat¶
- Homepage:
- Spack package:
- Versions:
- 1.4.0
- Build Dependencies:
- r-rhdf5, r, r-matrix, r-jsonlite, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-rhdf5, r, r-matrix, r-jsonlite, r-plyr
- Description:
- This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
r-biostrings¶
- Homepage:
- Spack package:
- Versions:
- 2.44.2
- Build Dependencies:
- r-s4vectors, r-biocgenerics, r, r-iranges, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r-s4vectors, r-biocgenerics, r, r-iranges, r-xvector
- Description:
- Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
r-biovizbase¶
- Homepage:
- Spack package:
- Versions:
- 1.24.0
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r-hmisc, r-scales, r-genomeinfodb, r-annotationdbi, r-variantannotation, r, r-iranges, r-rcolorbrewer, r-ensembldb, r-summarizedexperiment, r-genomicranges, r-genomicfeatures, r-s4vectors, r-dichromat, r-rsamtools, r-annotationfilter, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r-hmisc, r-scales, r-genomeinfodb, r-annotationdbi, r-variantannotation, r, r-iranges, r-rcolorbrewer, r-ensembldb, r-summarizedexperiment, r-genomicranges, r-genomicfeatures, r-s4vectors, r-dichromat, r-rsamtools, r-annotationfilter, r-biostrings
- Description:
- The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
r-bit¶
- Homepage:
- Spack package:
- Versions:
- 1.1-12
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A class for vectors of 1-bit booleans.
r-bit64¶
- Homepage:
- Spack package:
- Versions:
- 0.9-7
- Build Dependencies:
- r-bit, r
- Link Dependencies:
- r
- Run Dependencies:
- r-bit, r
- Description:
- Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.
r-bitops¶
- Homepage:
- Spack package:
- Versions:
- 1.0-6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions for bitwise operations on integer vectors.
r-blob¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- r-tibble, r
- Link Dependencies:
- r
- Run Dependencies:
- r-tibble, r
- Description:
- R's raw vector is useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.
r-bookdown¶
- Homepage:
- Spack package:
- Versions:
- 0.5
- Build Dependencies:
- r-rmarkdown, r-knitr, r-yaml, r-htmltools, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rmarkdown, r-knitr, r-yaml, r-htmltools, r
- Description:
- Output formats and utilities for authoring books and technical documents with R Markdown.
r-boot¶
- Homepage:
- Spack package:
- Versions:
- 1.3-20, 1.3-18
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
r-brew¶
- Homepage:
- Spack package:
- Versions:
- 1.0-6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.
r-broom¶
- Homepage:
- Spack package:
- Versions:
- 0.4.2
- Build Dependencies:
- r-reshape2, r, r-nlme, r-stringr, r-tidyr, r-dplyr, r-psych, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-reshape2, r, r-nlme, r-stringr, r-tidyr, r-dplyr, r-psych, r-plyr
- Description:
- Convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.
r-bsgenome¶
- Homepage:
- Spack package:
- Versions:
- 1.44.2
- Build Dependencies:
- r-biocgenerics, r-biostrings, r-genomicranges, r-genomeinfodb, r-s4vectors, r-iranges, r-rtracklayer, r-rsamtools, r, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-biostrings, r-genomicranges, r-genomeinfodb, r-s4vectors, r-iranges, r-rtracklayer, r-rsamtools, r, r-xvector
- Description:
- Infrastructure shared by all the Biostrings-based genome data packages.
r-bumphunter¶
- Homepage:
- Spack package:
- Versions:
- 1.16.0
- Build Dependencies:
- r, r-biocgenerics, r-iterators, r-genomeinfodb, r-limma, r-iranges, r-foreach, r-annotationdbi, r-dorng, r-genomicranges, r-genomicfeatures, r-matrixstats, r-s4vectors, r-locfit
- Link Dependencies:
- r
- Run Dependencies:
- r, r-biocgenerics, r-iterators, r-genomeinfodb, r-limma, r-iranges, r-foreach, r-annotationdbi, r-dorng, r-genomicranges, r-genomicfeatures, r-matrixstats, r-s4vectors, r-locfit
- Description:
- Tools for finding bumps in genomic data
r-c50¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0-24
- Build Dependencies:
- r-partykit, r
- Link Dependencies:
- r
- Run Dependencies:
- r-partykit, r
- Description:
- C5.0 decision trees and rule-based models for pattern recognition.
r-callr¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
r-car¶
- Homepage:
- Spack package:
- Versions:
- 2.1-4, 2.1-2
- Build Dependencies:
- r-mgcv, r-pbkrtest, r, r-nnet, r-quantreg, r-mass
- Link Dependencies:
- r
- Run Dependencies:
- r-mgcv, r-pbkrtest, r, r-nnet, r-quantreg, r-mass
- Description:
- Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.
r-caret¶
- Homepage:
- Spack package:
- Versions:
- 6.0-73, 6.0-70
- Build Dependencies:
- r-car, r-reshape2, r-foreach, r-lattice, r-ggplot2, r-nlme, r-plyr, r, r-modelmetrics
- Link Dependencies:
- r
- Run Dependencies:
- r-car, r-reshape2, r-foreach, r-lattice, r-ggplot2, r-nlme, r-plyr, r, r-modelmetrics
- Description:
- Misc functions for training and plotting classification and regression models.
r-category¶
- Homepage:
- Spack package:
- Versions:
- 2.42.1
- Build Dependencies:
- r-biocgenerics, r-rbgl, r-annotate, r-matrix, r-biobase, r-gseabase, r-dbi, r, r-annotationdbi, r-graph, r-genefilter
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-rbgl, r-annotate, r-matrix, r-biobase, r-gseabase, r-dbi, r, r-annotationdbi, r-graph, r-genefilter
- Description:
- A collection of tools for performing category analysis.
r-catools¶
- Homepage:
- Spack package:
- Versions:
- 1.17.1
- Build Dependencies:
- r-bitops, r
- Link Dependencies:
- r
- Run Dependencies:
- r-bitops, r
- Description:
- Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
r-cellranger¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- r-tibble, r-rematch, r
- Link Dependencies:
- r
- Run Dependencies:
- r-tibble, r-rematch, r
- Description:
- Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
r-checkmate¶
- Homepage:
- Spack package:
- Versions:
- 1.8.4
- Build Dependencies:
- r-backports, r
- Link Dependencies:
- r
- Run Dependencies:
- r-backports, r
- Description:
- Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
r-checkpoint¶
- Homepage:
- Spack package:
- Versions:
- 0.3.18, 0.3.15
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine.
r-chemometrics¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2, 1.4.1, 1.3.9, 1.3.8, 1.3.7
- Build Dependencies:
- r-pls, r-mclust, r-pcapp, r-rpart, r, r-e1071, r-som, r-robustbase, r-lars
- Link Dependencies:
- r
- Run Dependencies:
- r-pls, r-mclust, r-pcapp, r-rpart, r, r-e1071, r-som, r-robustbase, r-lars
- Description:
- R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).
r-chron¶
- Homepage:
- Spack package:
- Versions:
- 2.3-47
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Chronological objects which can handle dates and times.
r-circlize¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1, 0.4.0
- Build Dependencies:
- r-colorspace, r, r-globaloptions, r-shape
- Link Dependencies:
- r
- Run Dependencies:
- r-colorspace, r, r-globaloptions, r-shape
- Description:
- Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low- level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.
r-class¶
- Homepage:
- Spack package:
- Versions:
- 7.3-14
- Build Dependencies:
- r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-mass, r
- Description:
- Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
r-classint¶
- Homepage:
- Spack package:
- Versions:
- 0.1-24
- Build Dependencies:
- r-e1071, r, r-class
- Link Dependencies:
- r
- Run Dependencies:
- r-e1071, r, r-class
- Description:
- Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
r-cli¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r, r-assertthat, r-crayon
- Link Dependencies:
- r
- Run Dependencies:
- r, r-assertthat, r-crayon
- Description:
- A suite of tools designed to build attractive command line interfaces ('CLIs'). Includes tools for drawing rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives.
r-clipr¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- r-testthat, xclip, r, r-rstudioapi
- Link Dependencies:
- r, xclip
- Run Dependencies:
- r-testthat, r, r-rstudioapi
- Description:
- Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.
r-cluster¶
- Homepage:
- Spack package:
- Versions:
- 2.0.6, 2.0.5, 2.0.4
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
r-clusterprofiler¶
- Homepage:
- Spack package:
- Versions:
- 3.4.4
- Build Dependencies:
- r-qvalue, r-magrittr, r-gosemsim, r-ggplot2, r, r-rvcheck, r-go-db, r-dose, r-tidyr, r-annotationdbi, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-qvalue, r-magrittr, r-gosemsim, r-ggplot2, r, r-rvcheck, r-go-db, r-dose, r-tidyr, r-annotationdbi, r-plyr
- Description:
- This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.
r-coda¶
- Homepage:
- Spack package:
- Versions:
- 0.19-1
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.
r-codetools¶
- Homepage:
- Spack package:
- Versions:
- 0.2-15, 0.2-14
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Code analysis tools for R.
r-coin¶
- Homepage:
- Spack package:
- Versions:
- 1.1-3
- Build Dependencies:
- r-survival, r-multcomp, r-modeltools, r-mvtnorm, r
- Link Dependencies:
- r
- Run Dependencies:
- r-survival, r-multcomp, r-modeltools, r-mvtnorm, r
- Description:
- Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.
r-colorspace¶
- Homepage:
- Spack package:
- Versions:
- 1.3-2, 1.2-6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.
r-complexheatmap¶
- Homepage:
- Spack package:
- Versions:
- 1.14.0
- Build Dependencies:
- r-circlize, r-dendextend, r, r-colorspace, r-getoptlong, r-rcolorbrewer, r-globaloptions
- Link Dependencies:
- r
- Run Dependencies:
- r-circlize, r-dendextend, r, r-colorspace, r-getoptlong, r-rcolorbrewer, r-globaloptions
- Description:
- Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.
r-corpcor¶
- Homepage:
- Spack package:
- Versions:
- 1.6.9
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Efficient Estimation of Covariance and (Partial) Correlation
r-corrplot¶
- Homepage:
- Spack package:
- Versions:
- 0.77
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering.
r-covr¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1
- Build Dependencies:
- r-rex, r-withr, r, r-httr, r-jsonlite, r-crayon
- Link Dependencies:
- r
- Run Dependencies:
- r-rex, r-withr, r, r-httr, r-jsonlite, r-crayon
- Description:
- Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
r-cowplot¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0
- Build Dependencies:
- r-ggplot2, r, r-gtable, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r, r-gtable, r-plyr
- Description:
- Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package.
r-crayon¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4, 1.3.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.
r-crosstalk¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r-ggplot2, r, r-shiny, r-htmltools, r-jsonlite, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r, r-shiny, r-htmltools, r-jsonlite, r-lazyeval
- Description:
- Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files).
r-cubature¶
- Homepage:
- Spack package:
- Versions:
- 1.1-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Adaptive multivariate integration over hypercubes
r-cubist¶
- Homepage:
- Spack package:
- Versions:
- 0.0.19
- Build Dependencies:
- r-reshape2, r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-reshape2, r, r-lattice
- Description:
- Regression modeling using rules with added instance-based corrections
r-curl¶
- Homepage:
- Spack package:
- Versions:
- 3.0, 2.3, 1.0, 0.9.7
- Build Dependencies:
- curl, r
- Link Dependencies:
- curl, r
- Run Dependencies:
- r
- Description:
- The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.
r-data-table¶
- Homepage:
- Spack package:
- Versions:
- 1.10.4-2, 1.10.0, 1.9.6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.
r-dbi¶
- Homepage:
- Spack package:
- Versions:
- 0.7, 0.4-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
r-dbplyr¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- r-rlang, r-dbi, r-assertthat, r-glue, r-tibble, r-purrr, r, r-dplyr, r-r6
- Link Dependencies:
- r
- Run Dependencies:
- r-rlang, r-dbi, r-assertthat, r-glue, r-tibble, r-purrr, r, r-dplyr, r-r6
- Description:
- A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
r-delayedarray¶
- Homepage:
- Spack package:
- Versions:
- 0.2.7
- Build Dependencies:
- r-s4vectors, r-biocgenerics, r, r-iranges, r-matrixstats
- Link Dependencies:
- r
- Run Dependencies:
- r-s4vectors, r-biocgenerics, r, r-iranges, r-matrixstats
- Description:
- Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames. Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.
r-deldir¶
- Homepage:
- Spack package:
- Versions:
- 0.1-14
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.
r-dendextend¶
- Homepage:
- Spack package:
- Versions:
- 1.5.2
- Build Dependencies:
- r-magrittr, r-viridis, r-ggplot2, r, r-whisker, r-fpc
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-viridis, r-ggplot2, r, r-whisker, r-fpc
- Description:
- dendextend: Extending 'Dendrogram' Functionality in R
r-deoptim¶
- Homepage:
- Spack package:
- Versions:
- 2.2-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.
r-deoptimr¶
- Homepage:
- Spack package:
- Versions:
- 1.0-8
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An implementation of a bespoke jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems.
r-deseq¶
- Homepage:
- Spack package:
- Versions:
- 1.28.0
- Build Dependencies:
- r-biocgenerics, r-lattice, r-genefilter, r-biobase, r-locfit, r-geneplotter, r, r-rcolorbrewer, r-mass
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-lattice, r-genefilter, r-biobase, r-locfit, r-geneplotter, r, r-rcolorbrewer, r-mass
- Description:
- Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
r-deseq2¶
- Homepage:
- Spack package:
- Versions:
- 1.16.1
- Build Dependencies:
- r-rcpparmadillo, r-hmisc, r-genefilter, r-ggplot2, r-biocparallel, r-biocgenerics, r, r-iranges, r-biobase, r-locfit, r-genomicranges, r-s4vectors, r-summarizedexperiment, r-geneplotter, r-rcpp
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpparmadillo, r-hmisc, r-genefilter, r-ggplot2, r-biocparallel, r-biocgenerics, r, r-iranges, r-biobase, r-locfit, r-genomicranges, r-s4vectors, r-summarizedexperiment, r-geneplotter, r-rcpp
- Description:
- Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
r-desolve¶
- Homepage:
- Spack package:
- Versions:
- 1.20
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations.
r-devtools¶
- Homepage:
- Spack package:
- Versions:
- 1.12.0, 1.11.1
- Build Dependencies:
- r-digest, r-httr, r-withr, r, r-memoise, r-git2r, r-whisker, r-jsonlite, r-rstudioapi
- Link Dependencies:
- r
- Run Dependencies:
- r-digest, r-httr, r-withr, r, r-memoise, r-git2r, r-whisker, r-jsonlite, r-rstudioapi
- Description:
- Collection of package development tools.
r-diagrammer¶
- Homepage:
- Spack package:
- Versions:
- 0.8.4
- Build Dependencies:
- r-influencer, r-htmlwidgets, r, r-scales, r-stringr, r-visnetwork, r-igraph, r-rstudioapi
- Link Dependencies:
- r
- Run Dependencies:
- r-influencer, r-htmlwidgets, r, r-scales, r-stringr, r-visnetwork, r-igraph, r-rstudioapi
- Description:
- Create graph diagrams and flowcharts using R.
r-dichromat¶
- Homepage:
- Spack package:
- Versions:
- 2.0-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.
r-diffusionmap¶
- Homepage:
- Spack package:
- Versions:
- 1.1-0, 1.0-0, 0.0-2, 0.0-1
- Build Dependencies:
- r-matrix, r-scatterplot3d, r-igraph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r-scatterplot3d, r-igraph, r
- Description:
- Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.
r-digest¶
- Homepage:
- Spack package:
- Versions:
- 0.6.12, 0.6.11, 0.6.9
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. For xxhash, the implementation by Yann Collet is used. For murmurhash, an implementation by Shane Day is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.
r-diptest¶
- Homepage:
- Spack package:
- Versions:
- 0.75-7
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected
r-dnacopy¶
- Homepage:
- Spack package:
- Versions:
- 1.50.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.
r-do-db¶
- Homepage:
- Spack package:
- Versions:
- 2.9
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- A set of annotation maps describing the entire Disease Ontology assembled using data from DO.
r-domc¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4
- Build Dependencies:
- r-foreach, r-iterators, r
- Link Dependencies:
- r
- Run Dependencies:
- r-foreach, r-iterators, r
- Description:
- Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.
r-doparallel¶
- Homepage:
- Spack package:
- Versions:
- 1.0.11, 1.0.10
- Build Dependencies:
- r-foreach, r-iterators, r
- Link Dependencies:
- r
- Run Dependencies:
- r-foreach, r-iterators, r
- Description:
- Provides a parallel backend for the %dopar% function using the parallel package.
r-dorng¶
- Homepage:
- Spack package:
- Versions:
- 1.6.6
- Build Dependencies:
- r-foreach, r-iterators, r-pkgmaker, r-rngtools, r
- Link Dependencies:
- r
- Run Dependencies:
- r-foreach, r-iterators, r-pkgmaker, r-rngtools, r
- Description:
- Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple- recursive generator [L'Ecuyer (1999), <doi:10.1287/opre.47.1.159>]. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.
r-dose¶
- Homepage:
- Spack package:
- Versions:
- 3.2.0
- Build Dependencies:
- r-qvalue, r-ggplot2, r-reshape2, r, r-fgsea, r-biocparallel, r-annotationdbi, r-do-db, r-s4vectors, r-gosemsim, r-scales, r-igraph
- Link Dependencies:
- r
- Run Dependencies:
- r-qvalue, r-ggplot2, r-reshape2, r, r-fgsea, r-biocparallel, r-annotationdbi, r-do-db, r-s4vectors, r-gosemsim, r-scales, r-igraph
- Description:
- This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
r-downloader¶
- Homepage:
- Spack package:
- Versions:
- 0.4
- Build Dependencies:
- r-digest, r
- Link Dependencies:
- r
- Run Dependencies:
- r-digest, r
- Description:
- Provides a wrapper for the download.file function, making it possible to download files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. The 'RCurl' package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.
r-dplyr¶
- Homepage:
- Spack package:
- Versions:
- 0.7.3, 0.5.0
- Build Dependencies:
- r-magrittr, r-dbi, r-bindrcpp, r-assertthat, r-pkgconfig, r-tibble, r-r6, r, r-bh, r-plogr, r-glue, r-rcpp, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-dbi, r-bindrcpp, r-assertthat, r-pkgconfig, r-tibble, r-r6, r, r-bh, r-plogr, r-glue, r-rcpp, r-lazyeval
- Description:
- A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
r-dt¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- r-htmlwidgets, r-magrittr, r-htmltools, r
- Link Dependencies:
- r
- Run Dependencies:
- r-htmlwidgets, r-magrittr, r-htmltools, r
- Description:
- Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.
r-dtw¶
- Homepage:
- Spack package:
- Versions:
- 1.18-1, 1.17-1, 1.16, 1.15, 1.14-3
- Build Dependencies:
- r-proxy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-proxy, r
- Description:
- A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series.
r-dygraphs¶
- Homepage:
- Spack package:
- Versions:
- 0.9
- Build Dependencies:
- r-htmlwidgets, r-magrittr, r, r-zoo, r-xts
- Link Dependencies:
- r
- Run Dependencies:
- r-htmlwidgets, r-magrittr, r, r-zoo, r-xts
- Description:
- An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis- display and interactive features like zoom/pan and series/point highlighting.
r-e1071¶
- Homepage:
- Spack package:
- Versions:
- 1.6-7
- Build Dependencies:
- r, r-class
- Link Dependencies:
- r
- Run Dependencies:
- r, r-class
- Description:
- Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...
r-edger¶
- Homepage:
- Spack package:
- Versions:
- 3.18.1
- Build Dependencies:
- r-limma, r-locfit, r
- Link Dependencies:
- r
- Run Dependencies:
- r-limma, r-locfit, r
- Description:
- Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.
r-ellipse¶
- Homepage:
- Spack package:
- Versions:
- 0.3-8
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package contains various routines for drawing ellipses and ellipse- like confidence regions.
r-ensembldb¶
- Homepage:
- Spack package:
- Versions:
- 2.0.4
- Build Dependencies:
- r-rsqlite, r-biocgenerics, r-biostrings, r-genomeinfodb, r-dbi, r, r-annotationdbi, r-protgenerics, r-annotationfilter, r-iranges, r-biobase, r-curl, r-genomicfeatures, r-annotationhub, r-s4vectors, r-rtracklayer, r-rsamtools, r-genomicranges
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-biocgenerics, r-biostrings, r-genomeinfodb, r-dbi, r, r-annotationdbi, r-protgenerics, r-annotationfilter, r-iranges, r-biobase, r-curl, r-genomicfeatures, r-annotationhub, r-s4vectors, r-rtracklayer, r-rsamtools, r-genomicranges
- Description:
- The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.
r-ergm¶
- Homepage:
- Spack package:
- Versions:
- 3.7.1
- Build Dependencies:
- r-trust, r-matrix, r-lpsolve, r, r-network, r-coda, r-statnet-common, r-mass, r-robustbase
- Link Dependencies:
- r
- Run Dependencies:
- r-trust, r-matrix, r-lpsolve, r, r-network, r-coda, r-statnet-common, r-mass, r-robustbase
- Description:
- An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
r-evaluate¶
- Homepage:
- Spack package:
- Versions:
- 0.10.1, 0.10, 0.9
- Build Dependencies:
- r-stringr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-stringr, r
- Description:
- Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
r-expm¶
- Homepage:
- Spack package:
- Versions:
- 0.999-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Computation of the matrix exponential, logarithm, sqrt, and related quantities.
r-factoextra¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- r-factominer, r-abind, r-dendextend, r-ggpubr, r-ggrepel, r-ggplot2, r-tidyr, r, r-reshape2
- Link Dependencies:
- r
- Run Dependencies:
- r-factominer, r-abind, r-dendextend, r-ggpubr, r-ggrepel, r-ggplot2, r-tidyr, r, r-reshape2
- Description:
- factoextra: Extract and Visualize the Results of Multivariate Data Analyses
r-factominer¶
- Homepage:
- Spack package:
- Versions:
- 1.35
- Build Dependencies:
- r-car, r-scatterplot3d, r-leaps, r, r-knitr, r-flashclust, r-ellipse
- Link Dependencies:
- r
- Run Dependencies:
- r-car, r-scatterplot3d, r-leaps, r, r-knitr, r-flashclust, r-ellipse
- Description:
- FactoMineR: Multivariate Exploratory Data Analysis and Data Mining
r-ff¶
- Homepage:
- Spack package:
- Versions:
- 2.2-13
- Build Dependencies:
- r-bit, r
- Link Dependencies:
- r
- Run Dependencies:
- r-bit, r
- Description:
- memory-efficient storage of large data on disk and fast access functions.
r-fftwtools¶
- Homepage:
- Spack package:
- Versions:
- 0.9-8
- Build Dependencies:
- fftw, r
- Link Dependencies:
- fftw, r
- Run Dependencies:
- r
- Description:
- Provides a wrapper for several 'FFTW' functions. This package provides access to the two-dimensional 'FFT', the multivariate 'FFT', and the one-dimensional real to complex 'FFT' using the 'FFTW3' library. The package includes the functions fftw() and mvfftw() which are designed to mimic the functionality of the R functions fft() and mvfft(). The 'FFT' functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.
r-fgsea¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- r-ggplot2, r-gridextra, r, r-rcpp, r-data-table, r-biocparallel, r-fastmatch
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-gridextra, r, r-rcpp, r-data-table, r-biocparallel, r-fastmatch
- Description:
- The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
r-filehash¶
- Homepage:
- Spack package:
- Versions:
- 2.3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.
r-flashclust¶
- Homepage:
- Spack package:
- Versions:
- 1.01-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- flashClust: Implementation of optimal hierarchical clustering
r-flexmix¶
- Homepage:
- Spack package:
- Versions:
- 2.3-14
- Build Dependencies:
- r-modeltools, r
- Link Dependencies:
- r
- Run Dependencies:
- r-modeltools, r
- Description:
- flexmix: Flexible Mixture Modeling
r-fnn¶
- Homepage:
- Spack package:
- Versions:
- 1.1, 1.0, 0.6-4, 0.6-3, 0.6-2
- Build Dependencies:
- r-chemometrics, r-mvtnorm, r
- Link Dependencies:
- r
- Run Dependencies:
- r-chemometrics, r-mvtnorm, r
- Description:
- Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.
r-forcats¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- r-tibble, r, r-magrittr
- Link Dependencies:
- r
- Run Dependencies:
- r-tibble, r, r-magrittr
- Description:
- Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').
r-foreach¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3
- Build Dependencies:
- r-codetools, r-iterators, r
- Link Dependencies:
- r
- Run Dependencies:
- r-codetools, r-iterators, r
- Description:
- Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.
r-forecast¶
- Homepage:
- Spack package:
- Versions:
- 8.2
- Build Dependencies:
- r-magrittr, r-lmtest, r-ggplot2, r, r-timedate, r-nnet, r-zoo, r-fracdiff, r-colorspace, r-rcpp, r-tseries, r-rcpparmadillo
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-lmtest, r-ggplot2, r, r-timedate, r-nnet, r-zoo, r-fracdiff, r-colorspace, r-rcpp, r-tseries, r-rcpparmadillo
- Description:
- Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
r-foreign¶
- Homepage:
- Spack package:
- Versions:
- 0.8-66
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.
r-formatr¶
- Homepage:
- Spack package:
- Versions:
- 1.5, 1.4
- Build Dependencies:
- r-codetools, r, r-testit, r-shiny
- Link Dependencies:
- r
- Run Dependencies:
- r-codetools, r, r-testit, r-shiny
- Description:
- Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human- readable and tidy. There is also a Shiny app as a user interface in this package.
r-formula¶
- Homepage:
- Spack package:
- Versions:
- 1.2-2, 1.2-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Infrastructure for extended formulas with multiple parts on the right- hand side and/or multiple responses on the left-hand side.
r-fpc¶
- Homepage:
- Spack package:
- Versions:
- 2.1-10
- Build Dependencies:
- r-kernlab, r, r-flexmix, r-trimcluster, r-prabclus, r-diptest, r-mclust, r-mvtnorm, r-robustbase
- Link Dependencies:
- r
- Run Dependencies:
- r-kernlab, r, r-flexmix, r-trimcluster, r-prabclus, r-diptest, r-mclust, r-mvtnorm, r-robustbase
- Description:
- fpc: Flexible Procedures for Clustering
r-fracdiff¶
- Homepage:
- Spack package:
- Versions:
- 1.4-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989).
r-futile-logger¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3
- Build Dependencies:
- r-lambda-r, r-futile-options, r
- Link Dependencies:
- r
- Run Dependencies:
- r-lambda-r, r-futile-options, r
- Description:
- Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.
r-futile-options¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A scoped options management framework
r-gbm¶
- Homepage:
- Spack package:
- Versions:
- 2.1.3
- Build Dependencies:
- r, r-survival, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-survival, r-lattice
- Description:
- Generalized Boosted Regression Models.
r-gcrma¶
- Homepage:
- Spack package:
- Versions:
- 2.48.0
- Build Dependencies:
- r-biobase, r-affy, r-affyio, r-biostrings, r, r-biocinstaller, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-affy, r-affyio, r-biostrings, r, r-biocinstaller, r-xvector
- Description:
- Background adjustment using sequence information
r-gdata¶
- Homepage:
- Spack package:
- Versions:
- 2.18.0, 2.17.0
- Build Dependencies:
- r, r-gtools
- Link Dependencies:
- r
- Run Dependencies:
- r, r-gtools
- Description:
- Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS- Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').
r-gdsfmt¶
- Homepage:
- Spack package:
- Versions:
- 1.14.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random- access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.
r-geiger¶
- Homepage:
- Spack package:
- Versions:
- 2.0.6
- Build Dependencies:
- r-subplex, r-digest, r-coda, r-mvtnorm, r-ncbit, r-rcpp, r-colorspace, r-desolve, r, r-mass, r-ape
- Link Dependencies:
- r
- Run Dependencies:
- r-subplex, r-digest, r-coda, r-mvtnorm, r-ncbit, r-rcpp, r-colorspace, r-desolve, r, r-mass, r-ape
- Description:
- Methods for fitting macroevolutionary models to phylogenetic trees.
r-genefilter¶
- Homepage:
- Spack package:
- Versions:
- 1.58.1
- Build Dependencies:
- r-s4vectors, r-biobase, r-annotate, r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-s4vectors, r-biobase, r-annotate, r-annotationdbi, r
- Description:
- Some basic functions for filtering genes
r-geneplotter¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-biobase, r-annotate, r, r-biocgenerics, r-annotationdbi, r-rcolorbrewer, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-annotate, r, r-biocgenerics, r-annotationdbi, r-rcolorbrewer, r-lattice
- Description:
- Functions for plotting genomic data.
r-genomeinfodb¶
- Homepage:
- Spack package:
- Versions:
- 1.12.3
- Build Dependencies:
- r-biocgenerics, r, r-s4vectors, r-genomeinfodbdata, r-iranges, r-rcurl
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r, r-s4vectors, r-genomeinfodbdata, r-iranges, r-rcurl
- Description:
- Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
r-genomeinfodbdata¶
- Homepage:
- Spack package:
- Versions:
- 0.99.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.
r-genomicalignments¶
- Homepage:
- Spack package:
- Versions:
- 1.12.2
- Build Dependencies:
- r-biocgenerics, r-genomicranges, r-genomeinfodb, r-s4vectors, r-summarizedexperiment, r-iranges, r-rsamtools, r, r-biocparallel, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-genomicranges, r-genomeinfodb, r-s4vectors, r-summarizedexperiment, r-iranges, r-rsamtools, r, r-biocparallel, r-biostrings
- Description:
- Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
r-genomicfeatures¶
- Homepage:
- Spack package:
- Versions:
- 1.28.5
- Build Dependencies:
- r-rsqlite, r-biocgenerics, r-dbi, r-genomeinfodb, r-iranges, r, r-annotationdbi, r-biobase, r-biomart, r-genomicranges, r-s4vectors, r-rtracklayer, r-xvector, r-rcurl, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-biocgenerics, r-dbi, r-genomeinfodb, r-iranges, r, r-annotationdbi, r-biobase, r-biomart, r-genomicranges, r-s4vectors, r-rtracklayer, r-xvector, r-rcurl, r-biostrings
- Description:
- A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
r-genomicranges¶
- Homepage:
- Spack package:
- Versions:
- 1.28.6
- Build Dependencies:
- r-biocgenerics, r, r-s4vectors, r-genomeinfodb, r-iranges, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r, r-s4vectors, r-genomeinfodb, r-iranges, r-xvector
- Description:
- The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure.
r-geomorph¶
- Homepage:
- Spack package:
- Versions:
- 3.0.5
- Build Dependencies:
- r-ape, r-matrix, r, r-jpeg, r-rgl, r-geiger
- Link Dependencies:
- r
- Run Dependencies:
- r-ape, r-matrix, r, r-jpeg, r-rgl, r-geiger
- Description:
- Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
r-geoquery¶
- Homepage:
- Spack package:
- Versions:
- 2.42.0
- Build Dependencies:
- r-biobase, r-httr, r-xml, r-rcurl, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-httr, r-xml, r-rcurl, r
- Description:
- The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.
r-geosphere¶
- Homepage:
- Spack package:
- Versions:
- 1.5-5
- Build Dependencies:
- r-sp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-sp, r
- Description:
- Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
r-getopt¶
- Homepage:
- Spack package:
- Versions:
- 1.20.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Package designed to be used with Rscript to write "#!" shebang scripts that accept short and long flags/options. Many users will prefer using instead the packages optparse or argparse which add extra features like automatically generated help option and usage, support for default values, positional argument support, etc.
r-getoptlong¶
- Homepage:
- Spack package:
- Versions:
- 0.1.6
- Build Dependencies:
- perl, r-rjson, r-globaloptions, r
- Link Dependencies:
- perl, r
- Run Dependencies:
- r-rjson, r-globaloptions, r
- Description:
- This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.
r-ggally¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Build Dependencies:
- r-ggplot2, r, r-plyr, r-reshape, r-rcolorbrewer, r-progress, r-gtable
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r, r-plyr, r-reshape, r-rcolorbrewer, r-progress, r-gtable
- Description:
- The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.
r-ggbio¶
- Homepage:
- Spack package:
- Versions:
- 1.24.1
- Build Dependencies:
- r-genomicalignments, r-organismdbi, r-genomicfeatures, r-gridextra, r, r-iranges, r-rsamtools, r-annotationdbi, r-s4vectors, r-biovizbase, r-genomicranges, r-scales, r-rtracklayer, r-bsgenome, r-reshape2, r-hmisc, r-annotationfilter, r-variantannotation, r-genomeinfodb, r-ensembldb, r-biobase, r-ggally, r-summarizedexperiment, r-gtable, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-organismdbi, r-genomicfeatures, r-gridextra, r, r-iranges, r-rsamtools, r-annotationdbi, r-s4vectors, r-biovizbase, r-genomicranges, r-scales, r-rtracklayer, r-bsgenome, r-reshape2, r-hmisc, r-annotationfilter, r-variantannotation, r-genomeinfodb, r-ensembldb, r-biobase, r-ggally, r-summarizedexperiment, r-gtable, r-biostrings
- Description:
- The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
r-ggdendro¶
- Homepage:
- Spack package:
- Versions:
- 0.1-20
- Build Dependencies:
- r-ggplot2, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-mass, r
- Description:
- This is a set of tools for dendrograms and tree plots using 'ggplot2'. The 'ggplot2' philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device without exposing the data. The 'ggdendro' package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.
r-ggjoy¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0, 0.3.0, 0.2.0
- Build Dependencies:
- r-ggridges, r-ggplot2, r
- Link Dependencies:
- r
- Run Dependencies:
- r-ggridges, r-ggplot2, r
- Description:
- Joyplots provide a convenient way of visualizing changes in distributions over time or space.
r-ggmap¶
- Homepage:
- Spack package:
- Versions:
- 2.6.1
- Build Dependencies:
- r-ggplot2, r-reshape2, r, r-rgooglemaps, r-mapproj, r-scales, r-digest, r-proto, r-jpeg, r-geosphere, r-png, r-rjson, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-reshape2, r, r-rgooglemaps, r-mapproj, r-scales, r-digest, r-proto, r-jpeg, r-geosphere, r-png, r-rjson, r-plyr
- Description:
- A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.
r-ggplot2¶
- Homepage:
- Spack package:
- Versions:
- 2.2.1, 2.1.0
- Build Dependencies:
- r-reshape2, r-mass, r, r-scales, r-tibble, r-plyr, r-lazyeval, r-digest, r-gtable
- Link Dependencies:
- r
- Run Dependencies:
- r-reshape2, r-mass, r, r-scales, r-tibble, r-plyr, r-lazyeval, r-digest, r-gtable
- Description:
- An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples.
r-ggpubr¶
- Homepage:
- Spack package:
- Versions:
- 0.1.2
- Build Dependencies:
- r-ggplot2, r-ggsci, r, r-ggrepel, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-ggsci, r, r-ggrepel, r-plyr
- Description:
- ggpubr: 'ggplot2' Based Publication Ready Plots
r-ggrepel¶
- Homepage:
- Spack package:
- Versions:
- 0.6.5
- Build Dependencies:
- r-scales, r-ggplot2, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-scales, r-ggplot2, r-rcpp, r
- Description:
- ggrepel: Repulsive Text and Label Geoms for 'ggplot2'
r-ggridges¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1, 0.4.0
- Build Dependencies:
- r-ggplot2, r
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r
- Description:
- Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space.
r-ggsci¶
- Homepage:
- Spack package:
- Versions:
- 2.4
- Build Dependencies:
- r-scales, r-ggplot2, r
- Link Dependencies:
- r
- Run Dependencies:
- r-scales, r-ggplot2, r
- Description:
- ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
r-ggvis¶
- Homepage:
- Spack package:
- Versions:
- 0.4.3, 0.4.2
- Build Dependencies:
- r-magrittr, r-assertthat, r, r-dplyr, r-shiny, r-htmltools, r-jsonlite, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-assertthat, r, r-dplyr, r-shiny, r-htmltools, r-jsonlite, r-lazyeval
- Description:
- An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework from 'shiny' and web graphics from 'vega'.
r-gistr¶
- Homepage:
- Spack package:
- Versions:
- 0.3.6
- Build Dependencies:
- r-magrittr, r-httr, r-assertthat, r, r-rmarkdown, r-knitr, r-dplyr, r-jsonlite
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-httr, r-assertthat, r, r-rmarkdown, r-knitr, r-dplyr, r-jsonlite
- Description:
- Work with 'GitHub' 'gists' from 'R'. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not.
r-git2r¶
- Homepage:
- Spack package:
- Versions:
- 0.18.0, 0.15.0
- Build Dependencies:
- zlib, openssl, r
- Link Dependencies:
- zlib, openssl, r
- Run Dependencies:
- r
- Description:
- Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.
r-glmnet¶
- Homepage:
- Spack package:
- Versions:
- 2.0-13, 2.0-5
- Build Dependencies:
- r-foreach, r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-foreach, r-matrix, r
- Description:
- Extremely efficient procedures for fitting the entire lasso or elastic- net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path- wise fashion, as described in the paper linked to via the URL below.
r-globaloptions¶
- Homepage:
- Spack package:
- Versions:
- 0.0.12
- Build Dependencies:
- r-markdown, r-testthat, r-knitr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-markdown, r-testthat, r-knitr, r
- Description:
- It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
r-glue¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/stable/ manual/strings/#triple-quoted-string-literals>.
r-gmodels¶
- Homepage:
- Spack package:
- Versions:
- 2.16.2
- Build Dependencies:
- r-gdata, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gdata, r
- Description:
- Various R programming tools for model fitting.
r-gmp¶
- Homepage:
- Spack package:
- Versions:
- 0.5-13.1
- Build Dependencies:
- r, gmp
- Link Dependencies:
- r, gmp
- Run Dependencies:
- r
- Description:
- Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
r-go-db¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- A set of annotation maps describing the entire Gene Ontology assembled using data from GO.
r-googlevis¶
- Homepage:
- Spack package:
- Versions:
- 0.6.0
- Build Dependencies:
- r-jsonlite, r
- Link Dependencies:
- r
- Run Dependencies:
- r-jsonlite, r
- Description:
- R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
r-gosemsim¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- r-annotationdbi, r-go-db, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r-go-db, r-rcpp, r
- Description:
- The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
r-gostats¶
- Homepage:
- Spack package:
- Versions:
- 2.42.0
- Build Dependencies:
- r-category, r-biobase, r-annotate, r-annotationforge, r, r-go-db, r-rbgl, r-annotationdbi, r-graph
- Link Dependencies:
- r
- Run Dependencies:
- r-category, r-biobase, r-annotate, r-annotationforge, r, r-go-db, r-rbgl, r-annotationdbi, r-graph
- Description:
- A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
r-gplots¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1
- Build Dependencies:
- r, r-gdata, r-catools, r-kernsmooth, r-gtools
- Link Dependencies:
- r
- Run Dependencies:
- r, r-gdata, r-catools, r-kernsmooth, r-gtools
- Description:
- Various R Programming Tools for Plotting Data.
r-graph¶
- Homepage:
- Spack package:
- Versions:
- 1.54.0
- Build Dependencies:
- r-biocgenerics, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r
- Description:
- A package that implements some simple graph handling capabilities.
r-gridbase¶
- Homepage:
- Spack package:
- Versions:
- 0.4-7
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Integration of base and grid graphics.
r-gridextra¶
- Homepage:
- Spack package:
- Versions:
- 2.3, 2.2.1
- Build Dependencies:
- r-gtable, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gtable, r
- Description:
- Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.
r-gseabase¶
- Homepage:
- Spack package:
- Versions:
- 1.38.2
- Build Dependencies:
- r-biocgenerics, r-annotate, r-biobase, r, r-annotationdbi, r-graph, r-xml
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-annotate, r-biobase, r, r-annotationdbi, r-graph, r-xml
- Description:
- This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
r-gsubfn¶
- Homepage:
- Spack package:
- Versions:
- 0.6-6
- Build Dependencies:
- r-proto, r
- Link Dependencies:
- r
- Run Dependencies:
- r-proto, r
- Description:
- gsubfn is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable.
r-gtable¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Tools to make it easier to work with "tables" of 'grobs'.
r-gtools¶
- Homepage:
- Spack package:
- Versions:
- 3.5.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log- ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes.
r-gtrellis¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- r-circlize, r-iranges, r-genomicranges, r-getoptlong, r
- Link Dependencies:
- r
- Run Dependencies:
- r-circlize, r-iranges, r-genomicranges, r-getoptlong, r
- Description:
- Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.
r-gviz¶
- Homepage:
- Spack package:
- Versions:
- 1.20.0
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r, r-iranges, r-rsamtools, r-annotationdbi, r-digest, r-biovizbase, r-genomicranges, r-s4vectors, r-rtracklayer, r-bsgenome, r-biostrings, r-genomeinfodb, r-rcolorbrewer, r-biobase, r-biomart, r-latticeextra, r-genomicfeatures, r-matrixstats, r-xvector, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r, r-iranges, r-rsamtools, r-annotationdbi, r-digest, r-biovizbase, r-genomicranges, r-s4vectors, r-rtracklayer, r-bsgenome, r-biostrings, r-genomeinfodb, r-rcolorbrewer, r-biobase, r-biomart, r-latticeextra, r-genomicfeatures, r-matrixstats, r-xvector, r-lattice
- Description:
- Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
r-haven¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- r-readr, r-forcats, r, r-tibble, r-rcpp, r-hms
- Link Dependencies:
- r
- Run Dependencies:
- r-readr, r-forcats, r, r-tibble, r-rcpp, r-hms
- Description:
- Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
r-hexbin¶
- Homepage:
- Spack package:
- Versions:
- 1.27.1
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
r-highr¶
- Homepage:
- Spack package:
- Versions:
- 0.6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.
r-hmisc¶
- Homepage:
- Spack package:
- Versions:
- 4.0-3
- Build Dependencies:
- r-ggplot2, r-lattice, r, r-data-table, r-survival, r-base64enc, r-htmltable, r-latticeextra, r-gridextra, r-acepack, r-viridis, r-htmltools, r-formula
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-lattice, r, r-data-table, r-survival, r-base64enc, r-htmltable, r-latticeextra, r-gridextra, r-acepack, r-viridis, r-htmltools, r-formula
- Description:
- Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
r-hms¶
- Homepage:
- Spack package:
- Versions:
- 0.3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
r-htmltable¶
- Homepage:
- Spack package:
- Versions:
- 1.9
- Build Dependencies:
- r-magrittr, r-checkmate, r, r-htmlwidgets, r-stringr, r-knitr
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-checkmate, r, r-htmlwidgets, r-stringr, r-knitr
- Description:
- Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package also contains a few text formatting functions that help outputting text compatible with HTML/'LaTeX'.
r-htmltools¶
- Homepage:
- Spack package:
- Versions:
- 0.3.6, 0.3.5
- Build Dependencies:
- r-digest, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-digest, r-rcpp, r
- Description:
- Tools for HTML generation and output.
r-htmlwidgets¶
- Homepage:
- Spack package:
- Versions:
- 0.9, 0.8, 0.6
- Build Dependencies:
- r-htmltools, r-jsonlite, r-yaml, r
- Link Dependencies:
- r
- Run Dependencies:
- r-htmltools, r-jsonlite, r-yaml, r
- Description:
- A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.
r-httpuv¶
- Homepage:
- Spack package:
- Versions:
- 1.3.5, 1.3.3
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http- parser license information.)
r-httr¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1, 1.2.1, 1.1.0
- Build Dependencies:
- r-curl, r, r-r6, r-openssl, r-jsonlite, r-mime
- Link Dependencies:
- r
- Run Dependencies:
- r-curl, r, r-r6, r-openssl, r-jsonlite, r-mime
- Description:
- Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
r-hwriter¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Easy-to-use and versatile functions to output R objects in HTML format.
r-hypergraph¶
- Homepage:
- Spack package:
- Versions:
- 1.48.0
- Build Dependencies:
- r-graph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-graph, r
- Description:
- A package that implements some simple capabilities for representing and manipulating hypergraphs.
r-ica¶
- Homepage:
- Spack package:
- Versions:
- 1.0-1, 1.0-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
r-igraph¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- r-magrittr, r-nmf, r-matrix, r-irlba, r, gmp, libxml2
- Link Dependencies:
- gmp, libxml2, r
- Run Dependencies:
- r-magrittr, r-nmf, r-matrix, r-irlba, r
- Description:
- Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
r-illuminaio¶
- Homepage:
- Spack package:
- Versions:
- 0.18.0
- Build Dependencies:
- r-base64, r
- Link Dependencies:
- r
- Run Dependencies:
- r-base64, r
- Description:
- Tools for parsing Illumina's microarray output files, including IDAT.
r-impute¶
- Homepage:
- Spack package:
- Versions:
- 1.50.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Imputation for microarray data (currently KNN only).
r-influencer¶
- Homepage:
- Spack package:
- Versions:
- 0.1.0
- Build Dependencies:
- r-igraph, r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-igraph, r-matrix, r
- Description:
- Provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. On Unix systems, the betweenness, Key Players, and bridging implementations are parallelized with OpenMP, which may run faster on systems which have OpenMP configured.
r-inline¶
- Homepage:
- Spack package:
- Versions:
- 0.3.14
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.
r-interactivedisplaybase¶
- Homepage:
- Spack package:
- Versions:
- 1.14.0
- Build Dependencies:
- r-biocgenerics, r-shiny, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-shiny, r
- Description:
- The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.
r-ipred¶
- Homepage:
- Spack package:
- Versions:
- 0.9-5
- Build Dependencies:
- r-prodlim, r-rpart, r, r-nnet, r-survival, r-mass, r-class
- Link Dependencies:
- r
- Run Dependencies:
- r-prodlim, r-rpart, r, r-nnet, r-survival, r-mass, r-class
- Description:
- Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.
r-iranges¶
- Homepage:
- Spack package:
- Versions:
- 2.10.5
- Build Dependencies:
- r-s4vectors, r-biocgenerics, r
- Link Dependencies:
- r
- Run Dependencies:
- r-s4vectors, r-biocgenerics, r
- Description:
- Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
r-irdisplay¶
- Homepage:
- Spack package:
- Versions:
- 0.4.4
- Build Dependencies:
- r-repr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-repr, r
- Description:
- An interface to the rich display capabilities of Jupyter front-ends (e.g. 'Jupyter Notebook') Designed to be used from a running IRkernel session
r-irkernel¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- r-repr, r-digest, r-pbdzmq, r, r-irdisplay, r-devtools, r-crayon, r-evaluate, r-uuid
- Link Dependencies:
- r
- Run Dependencies:
- r-repr, r-digest, r-pbdzmq, r, r-irdisplay, r-devtools, r-crayon, r-evaluate, r-uuid
- Description:
- R kernel for Jupyter
r-irlba¶
- Homepage:
- Spack package:
- Versions:
- 2.1.2, 2.0.0
- Build Dependencies:
- r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r
- Description:
- Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principal component analysis of large sparse or dense matrices.
r-iso¶
- Homepage:
- Spack package:
- Versions:
- 0.0-17
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.
r-iterators¶
- Homepage:
- Spack package:
- Versions:
- 1.0.8
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.
r-janitor¶
- Homepage:
- Spack package:
- Versions:
- 0.3.0
- Build Dependencies:
- r-magrittr, r-tidyr, r-dplyr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-tidyr, r-dplyr, r
- Description:
- The main janitor functions can: perfectly format data.frame column names; provide quick one- and two-variable tabulations (i.e., frequency tables and crosstabs); and isolate duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and- report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to- intermediate R users in mind and is optimized for user-friendliness. Advanced R users can already do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.
r-jpeg¶
- Homepage:
- Spack package:
- Versions:
- 0.1-8
- Build Dependencies:
- jpeg, r
- Link Dependencies:
- jpeg, r
- Run Dependencies:
- r
- Description:
- This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.
r-jsonlite¶
- Homepage:
- Spack package:
- Versions:
- 1.5, 1.2, 1.0, 0.9.21
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
r-kegg-db¶
- Homepage:
- Spack package:
- Versions:
- 3.2.3
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- A set of annotation maps for KEGG assembled using data from KEGG.
r-kegggraph¶
- Homepage:
- Spack package:
- Versions:
- 1.38.1
- Build Dependencies:
- r-graph, r-xml, r
- Link Dependencies:
- r
- Run Dependencies:
- r-graph, r-xml, r
- Description:
- KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
r-keggrest¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r-png, r, r-httr, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-png, r, r-httr, r-biostrings
- Description:
- This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.
r-kernlab¶
- Homepage:
- Spack package:
- Versions:
- 0.9-25
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
r-kernsmooth¶
- Homepage:
- Spack package:
- Versions:
- 2.23-15
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions for kernel smoothing (and density estimation).
r-kknn¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- r-igraph, r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-igraph, r-matrix, r
- Description:
- Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
r-knitr¶
- Homepage:
- Spack package:
- Versions:
- 1.17, 1.14, 0.6
- Build Dependencies:
- r-markdown, r-digest, r-yaml, r, r-stringr, r-evaluate, r-formatr, r-highr
- Link Dependencies:
- r
- Run Dependencies:
- r-markdown, r-digest, r-yaml, r, r-stringr, r-evaluate, r-formatr, r-highr
- Description:
- Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
r-labeling¶
- Homepage:
- Spack package:
- Versions:
- 0.3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides a range of axis labeling algorithms.
r-lambda-r¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
r-laplacesdemon¶
- Homepage:
- Spack package:
- Versions:
- 16.0.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
r-lars¶
- Homepage:
- Spack package:
- Versions:
- 1.2, 1.1, 0.9-8
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.
r-lattice¶
- Homepage:
- Spack package:
- Versions:
- 0.20-35, 0.20-34
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.
r-latticeextra¶
- Homepage:
- Spack package:
- Versions:
- 0.6-28
- Build Dependencies:
- r, r-rcolorbrewer, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-rcolorbrewer, r-lattice
- Description:
- Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.
r-lava¶
- Homepage:
- Spack package:
- Versions:
- 1.4.7
- Build Dependencies:
- r-numderiv, r-survival, r
- Link Dependencies:
- r
- Run Dependencies:
- r-numderiv, r-survival, r
- Description:
- Estimation and simulation of latent variable models.
r-lazyeval¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.
r-leaflet¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- r-base64enc, r-magrittr, r-sp, r-raster, r-scales, r, r-htmlwidgets, r-png, r-htmltools, r-rcolorbrewer, r-markdown
- Link Dependencies:
- r
- Run Dependencies:
- r-base64enc, r-magrittr, r-sp, r-raster, r-scales, r, r-htmlwidgets, r-png, r-htmltools, r-rcolorbrewer, r-markdown
- Description:
- Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.
r-leaps¶
- Homepage:
- Spack package:
- Versions:
- 3.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- leaps: Regression Subset Selection
r-learnbayes¶
- Homepage:
- Spack package:
- Versions:
- 2.15
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- LearnBayes contains a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
r-limma¶
- Homepage:
- Spack package:
- Versions:
- 3.32.10, 3.32.6
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Data analysis, linear models and differential expression for microarray data.
r-lme4¶
- Homepage:
- Spack package:
- Versions:
- 1.1-12
- Build Dependencies:
- r-rcppeigen, r-nloptr, r-matrix, r, r-nlme, r-minqa, r-rcpp, r-mass, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-rcppeigen, r-nloptr, r-matrix, r, r-nlme, r-minqa, r-rcpp, r-mass, r-lattice
- Description:
- Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
r-lmtest¶
- Homepage:
- Spack package:
- Versions:
- 0.9-34
- Build Dependencies:
- r-zoo, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r
- Description:
- A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.
r-locfit¶
- Homepage:
- Spack package:
- Versions:
- 1.5-9.1
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Local regression, likelihood and density estimation.
r-log4r¶
- Homepage:
- Spack package:
- Versions:
- 0.2
- Build Dependencies:
- r-testthat, r
- Link Dependencies:
- r
- Run Dependencies:
- r-testthat, r
- Description:
- logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.
r-lpsolve¶
- Homepage:
- Spack package:
- Versions:
- 5.6.13
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve
r-lsei¶
- Homepage:
- Spack package:
- Versions:
- 1.2-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first. It is developed based on the 'Fortran' program of Lawson and Hanson (1974, 1995), which is public domain and available at <http://www.netlib.org/lawson-hanson>.
r-lubridate¶
- Homepage:
- Spack package:
- Versions:
- 1.5.6
- Build Dependencies:
- r-stringr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-stringr, r
- Description:
- Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and timespan objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.
r-magic¶
- Homepage:
- Spack package:
- Versions:
- 1.5-6
- Build Dependencies:
- r-abind, r
- Link Dependencies:
- r
- Run Dependencies:
- r-abind, r
- Description:
- A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.
r-magrittr¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette.
r-makecdfenv¶
- Homepage:
- Spack package:
- Versions:
- 1.52.0
- Build Dependencies:
- r-biobase, r-affy, r-zlibbioc, r-affyio, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-affy, r-zlibbioc, r-affyio, r
- Description:
- This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
r-maldiquant¶
- Homepage:
- Spack package:
- Versions:
- 1.16.4
- Build Dependencies:
- r-testthat, r-knitr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-testthat, r-knitr, r
- Description:
- A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two- dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
r-mapproj¶
- Homepage:
- Spack package:
- Versions:
- 1.2-4
- Build Dependencies:
- r-maps, r
- Link Dependencies:
- r
- Run Dependencies:
- r-maps, r
- Description:
- Converts latitude/longitude into projected coordinates.
r-maps¶
- Homepage:
- Spack package:
- Versions:
- 3.1.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').
r-maptools¶
- Homepage:
- Spack package:
- Versions:
- 0.8-39
- Build Dependencies:
- r-foreign, r-sp, r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-foreign, r-sp, r, r-lattice
- Description:
- Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
r-markdown¶
- Homepage:
- Spack package:
- Versions:
- 0.8, 0.7.7
- Build Dependencies:
- r, r-mime
- Link Dependencies:
- r
- Run Dependencies:
- r, r-mime
- Description:
- Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.
r-mass¶
- Homepage:
- Spack package:
- Versions:
- 7.3-47, 7.3-45
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
r-matrix¶
- Homepage:
- Spack package:
- Versions:
- 1.2-11, 1.2-8, 1.2-6
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.
r-matrixmodels¶
- Homepage:
- Spack package:
- Versions:
- 0.4-1
- Build Dependencies:
- r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r
- Description:
- Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.
r-matrixstats¶
- Homepage:
- Spack package:
- Versions:
- 0.52.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
r-mclust¶
- Homepage:
- Spack package:
- Versions:
- 5.3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- mclust: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
r-mcmcglmm¶
- Homepage:
- Spack package:
- Versions:
- 2.25
- Build Dependencies:
- r-cubature, r-coda, r-matrix, r, r-corpcor, r-tensora, r-ape
- Link Dependencies:
- r
- Run Dependencies:
- r-cubature, r-coda, r-matrix, r, r-corpcor, r-tensora, r-ape
- Description:
- MCMC Generalised Linear Mixed Models.
r-mda¶
- Homepage:
- Spack package:
- Versions:
- 0.4-9
- Build Dependencies:
- r, r-class
- Link Dependencies:
- r
- Run Dependencies:
- r, r-class
- Description:
- Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.
r-memoise¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0, 1.0.0
- Build Dependencies:
- r-digest, r
- Link Dependencies:
- r
- Run Dependencies:
- r-digest, r
- Description:
- Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.
r-mergemaid¶
- Homepage:
- Spack package:
- Versions:
- 2.48.0
- Build Dependencies:
- r-biobase, r-survival, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-survival, r-mass, r
- Description:
- The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross- validate associations of gene expression data with survival.
r-methodss3¶
- Homepage:
- Spack package:
- Versions:
- 1.7.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.
r-mgcv¶
- Homepage:
- Spack package:
- Versions:
- 1.8-16, 1.8-13
- Build Dependencies:
- r-nlme, r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-nlme, r-matrix, r
- Description:
- GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.
r-mime¶
- Homepage:
- Spack package:
- Versions:
- 0.5, 0.4
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.
r-minfi¶
- Homepage:
- Spack package:
- Versions:
- 1.22.1
- Build Dependencies:
- r-biocgenerics, r-siggenes, r-beanplot, r, r-nlme, r-matrixstats, r-bumphunter, r-iranges, r-mclust, r-preprocesscore, r-quadprog, r-biobase, r-genomicranges, r-s4vectors, r-data-table, r-nor1mix, r-genefilter, r-genomeinfodb, r-reshape, r-limma, r-rcolorbrewer, r-illuminaio, r-biostrings, r-geoquery, r-summarizedexperiment, r-mass, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-siggenes, r-beanplot, r, r-nlme, r-matrixstats, r-bumphunter, r-iranges, r-mclust, r-preprocesscore, r-quadprog, r-biobase, r-genomicranges, r-s4vectors, r-data-table, r-nor1mix, r-genefilter, r-genomeinfodb, r-reshape, r-limma, r-rcolorbrewer, r-illuminaio, r-biostrings, r-geoquery, r-summarizedexperiment, r-mass, r-lattice
- Description:
- Tools to analyze & visualize Illumina Infinium methylation arrays.
r-minqa¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.
r-mixtools¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0, 1.0.4
- Build Dependencies:
- r-segmented, r-survival, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-segmented, r-survival, r-mass, r
- Description:
- mixtools: Tools for Analyzing Finite Mixture Models Analyzes finite mixture models for various parametric and semiparametric settings.
r-mlbench¶
- Homepage:
- Spack package:
- Versions:
- 2.1-1
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.
r-mlinterfaces¶
- Homepage:
- Spack package:
- Versions:
- 1.56.0
- Build Dependencies:
- r-pls, r-biocgenerics, r-genefilter, r-sfsmisc, r, r-rda, r-hwriter, r-gbm, r-rcolorbrewer, r-biobase, r-gdata, r-threejs, r-mlbench, r-ggvis, r-shiny, r-fpc
- Link Dependencies:
- r
- Run Dependencies:
- r-pls, r-biocgenerics, r-genefilter, r-sfsmisc, r, r-rda, r-hwriter, r-gbm, r-rcolorbrewer, r-biobase, r-gdata, r-threejs, r-mlbench, r-ggvis, r-shiny, r-fpc
- Description:
- This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.
r-mnormt¶
- Homepage:
- Spack package:
- Versions:
- 1.5-5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
r-modelmetrics¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- Collection of metrics for evaluating models written in C++ using 'Rcpp'.
r-modelr¶
- Homepage:
- Spack package:
- Versions:
- 0.1.1
- Build Dependencies:
- r-magrittr, r-broom, r, r-tibble, r-purrr, r-tidyr, r-dplyr, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-broom, r, r-tibble, r-purrr, r-tidyr, r-dplyr, r-lazyeval
- Description:
- Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.
r-modeltools¶
- Homepage:
- Spack package:
- Versions:
- 0.2-21
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A collection of tools to deal with statistical models.
r-mpm¶
- Homepage:
- Spack package:
- Versions:
- 1.0-22
- Build Dependencies:
- r-kernsmooth, r
- Link Dependencies:
- r
- Run Dependencies:
- r-kernsmooth, r
- Description:
- Exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.
r-msnbase¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- r-protgenerics, r-biocgenerics, r-affy, r-ggplot2, r-biocparallel, r-xml, r, r-iranges, r-vsn, r-biobase, r-digest, r-impute, r-maldiquant, r-s4vectors, r-mzr, r-mzid, r-plyr, r-rcpp, r-pcamethods, r-preprocesscore, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-protgenerics, r-biocgenerics, r-affy, r-ggplot2, r-biocparallel, r-xml, r, r-iranges, r-vsn, r-biobase, r-digest, r-impute, r-maldiquant, r-s4vectors, r-mzr, r-mzid, r-plyr, r-rcpp, r-pcamethods, r-preprocesscore, r-lattice
- Description:
- Manipulation, processing and visualisation of mass spectrometry and proteomics data.
r-multcomp¶
- Homepage:
- Spack package:
- Versions:
- 1.4-6
- Build Dependencies:
- r-codetools, r, r-sandwich, r-survival, r-th-data, r-mvtnorm
- Link Dependencies:
- r
- Run Dependencies:
- r-codetools, r, r-sandwich, r-survival, r-th-data, r-mvtnorm
- Description:
- Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
r-multtest¶
- Homepage:
- Spack package:
- Versions:
- 2.32.0
- Build Dependencies:
- r-biocgenerics, r, r-biobase
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r, r-biobase
- Description:
- Resampling-based multiple hypothesis testing
r-munsell¶
- Homepage:
- Spack package:
- Versions:
- 0.4.3
- Build Dependencies:
- r-colorspace, r
- Link Dependencies:
- r
- Run Dependencies:
- r-colorspace, r
- Description:
- Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.
r-mvtnorm¶
- Homepage:
- Spack package:
- Versions:
- 1.0-6, 1.0-5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Computes multivariate normal and t probabilities, quantiles, random deviates and densities.
r-mzid¶
- Homepage:
- Spack package:
- Versions:
- 1.14.0
- Build Dependencies:
- r-protgenerics, r-doparallel, r-iterators, r, r-foreach, r-xml, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-protgenerics, r-doparallel, r-iterators, r, r-foreach, r-xml, r-plyr
- Description:
- A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.
r-mzr¶
- Homepage:
- Spack package:
- Versions:
- 2.10.0
- Build Dependencies:
- r-protgenerics, r-biobase, r-zlibbioc, r, r-biocgenerics, r-rcpp, netcdf
- Link Dependencies:
- netcdf, r
- Run Dependencies:
- r-protgenerics, r-biobase, r-zlibbioc, r, r-biocgenerics, r-rcpp
- Description:
- mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
r-nanotime¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- r-zoo, r-rcppcctz, r-bit64, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-rcppcctz, r-bit64, r
- Description:
- Full 64-bit resolution date and time support with resolution up to nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.
r-ncbit¶
- Homepage:
- Spack package:
- Versions:
- 2013.03.29
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Making NCBI taxonomic data locally available and searchable as an R object.
r-ncdf4¶
- Homepage:
- Spack package:
- Versions:
- 1.15
- Build Dependencies:
- netcdf, r
- Link Dependencies:
- netcdf, r
- Run Dependencies:
- r
- Description:
- Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.
r-network¶
- Homepage:
- Spack package:
- Versions:
- 1.13.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
r-networkd3¶
- Homepage:
- Spack package:
- Versions:
- 0.2.12
- Build Dependencies:
- r-htmlwidgets, r-magrittr, r-igraph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-htmlwidgets, r-magrittr, r-igraph, r
- Description:
- Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.
r-nlme¶
- Homepage:
- Spack package:
- Versions:
- 3.1-131, 3.1-130, 3.1-128
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Fit and compare Gaussian linear and nonlinear mixed-effects models.
r-nloptr¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- r-testthat, r
- Link Dependencies:
- r
- Run Dependencies:
- r-testthat, r
- Description:
- nloptr is an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See http://ab- initio.mit.edu/wiki/index.php/NLopt _Introduction for more information on the available algorithms. During installation on Unix the NLopt code is downloaded and compiled from the NLopt website.
r-nmf¶
- Homepage:
- Spack package:
- Versions:
- 0.20.6
- Build Dependencies:
- r-ggplot2, r-doparallel, r-cluster, r, r-foreach, r-reshape2, r-rcolorbrewer, r-digest, r-rngtools, r-registry, r-colorspace, r-stringr, r-gridbase, r-pkgmaker
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-doparallel, r-cluster, r, r-foreach, r-reshape2, r-rcolorbrewer, r-digest, r-rngtools, r-registry, r-colorspace, r-stringr, r-gridbase, r-pkgmaker
- Description:
- Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines..
r-nnet¶
- Homepage:
- Spack package:
- Versions:
- 7.3-12
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
r-nnls¶
- Homepage:
- Spack package:
- Versions:
- 1.4
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An R interface to the Lawson-Hanson implementation of an algorithm for non-negative least squares (NNLS). Also allows the combination of non- negative and non-positive constraints.
r-nor1mix¶
- Homepage:
- Spack package:
- Versions:
- 1.2-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Efficient random number generation and graphics; now fitting to data by ML (Maximum Likelihood) or EM estimation.
r-np¶
- Homepage:
- Spack package:
- Versions:
- 0.60-2
- Build Dependencies:
- r-cubature, r-boot, r
- Link Dependencies:
- r
- Run Dependencies:
- r-cubature, r-boot, r
- Description:
- This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).
r-numderiv¶
- Homepage:
- Spack package:
- Versions:
- 2016.8-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Methods for calculating (usually) accurate numerical first and second order derivatives.
r-oligoclasses¶
- Homepage:
- Spack package:
- Versions:
- 1.38.0
- Build Dependencies:
- r-rsqlite, r-biocgenerics, r, r-foreach, r-iranges, r-biobase, r-biocinstaller, r-genomicranges, r-ff, r-s4vectors, r-summarizedexperiment, r-affyio, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-biocgenerics, r, r-foreach, r-iranges, r-biobase, r-biocinstaller, r-genomicranges, r-ff, r-s4vectors, r-summarizedexperiment, r-affyio, r-biostrings
- Description:
- This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
r-oo¶
- Homepage:
- Spack package:
- Versions:
- 1.21.0
- Build Dependencies:
- r-methodss3, r
- Link Dependencies:
- r
- Run Dependencies:
- r-methodss3, r
- Description:
- Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
r-openssl¶
- Homepage:
- Spack package:
- Versions:
- 0.9.7, 0.9.6, 0.9.4
- Build Dependencies:
- openssl, r
- Link Dependencies:
- openssl, r
- Run Dependencies:
- r
- Description:
- Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
r-org-hs-eg-db¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.
r-organismdbi¶
- Homepage:
- Spack package:
- Versions:
- 1.18.1
- Build Dependencies:
- r-annotationdbi, r-biocgenerics, r-dbi, r, r-rbgl, r-iranges, r-graph, r-biobase, r-genomicranges, r-genomicfeatures, r-s4vectors, r-biocinstaller
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r-biocgenerics, r-dbi, r, r-rbgl, r-iranges, r-graph, r-biobase, r-genomicranges, r-genomicfeatures, r-s4vectors, r-biocinstaller
- Description:
- The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
r-packrat¶
- Homepage:
- Spack package:
- Versions:
- 0.4.8-1, 0.4.7-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Manage the R packages your project depends on in an isolated, portable, and reproducible way.
r-pacman¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1
- Build Dependencies:
- r-devtools, r
- Link Dependencies:
- r
- Run Dependencies:
- r-devtools, r
- Description:
- Tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.
r-pamr¶
- Homepage:
- Spack package:
- Versions:
- 1.55
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Some functions for sample classification in microarrays.
r-party¶
- Homepage:
- Spack package:
- Versions:
- 1.1-2
- Build Dependencies:
- r-zoo, r-coin, r, r-sandwich, r-strucchange, r-survival, r-modeltools, r-mvtnorm
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-coin, r, r-sandwich, r-strucchange, r-survival, r-modeltools, r-mvtnorm
- Description:
- A computational toolbox for recursive partitioning.
r-partykit¶
- Homepage:
- Spack package:
- Versions:
- 1.1-1
- Build Dependencies:
- r, r-survival, r-formula
- Link Dependencies:
- r
- Run Dependencies:
- r, r-survival, r-formula
- Description:
- A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure.
r-pathview¶
- Homepage:
- Spack package:
- Versions:
- 1.16.7
- Build Dependencies:
- r-keggrest, r-annotationdbi, r-kegggraph, r, r-rgraphviz, r-png, r-org-hs-eg-db, r-graph, r-xml
- Link Dependencies:
- r
- Run Dependencies:
- r-keggrest, r-annotationdbi, r-kegggraph, r, r-rgraphviz, r-png, r-org-hs-eg-db, r-graph, r-xml
- Description:
- Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
r-pbapply¶
- Homepage:
- Spack package:
- Versions:
- 1.3-3, 1.3-2, 1.3-1, 1.3-0, 1.2-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A lightweight package that adds progress bar to vectorized R apply functions.
r-pbdzmq¶
- Homepage:
- Spack package:
- Versions:
- 0.2-4
- Build Dependencies:
- r-r6, zeromq, r
- Link Dependencies:
- zeromq, r
- Run Dependencies:
- r-r6, r
- Description:
- 'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.
r-pbkrtest¶
- Homepage:
- Spack package:
- Versions:
- 0.4-6, 0.4-4
- Build Dependencies:
- r-lme4, r-matrix, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-lme4, r-matrix, r-mass, r
- Description:
- Test in mixed effects models. Attention is on mixed effects models as implemented in the 'lme4' package. This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.
r-pcamethods¶
- Homepage:
- Spack package:
- Versions:
- 1.68.0
- Build Dependencies:
- r-biobase, r, r-rcpp, r-mass, r-biocgenerics
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r, r-rcpp, r-mass, r-biocgenerics
- Description:
- Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.
r-pcapp¶
- Homepage:
- Spack package:
- Versions:
- 1.9-72, 1.9-70, 1.9-61, 1.9-60, 1.9-50
- Build Dependencies:
- r-mvtnorm, r
- Link Dependencies:
- r
- Run Dependencies:
- r-mvtnorm, r
- Description:
- Provides functions for robust PCA by projection pursuit.
r-permute¶
- Homepage:
- Spack package:
- Versions:
- 0.9-4
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely- exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
r-pfam-db¶
- Homepage:
- Spack package:
- Versions:
- 3.4.1
- Build Dependencies:
- r-annotationdbi, r
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r
- Description:
- A set of protein ID mappings for PFAM assembled using data from public repositories.
r-phantompeakqualtools¶
- Homepage:
- Spack package:
- Versions:
- 1.14
- Build Dependencies:
- r-rsamtools, boost, r, r-catools, r-snowfall, r-bitops, r-snow
- Link Dependencies:
- boost, r
- Run Dependencies:
- r-catools, r-snow, r, r-rsamtools, r-snowfall, r-bitops
- Description:
- Computes informative enrichment and quality measures for ChIP-seq/DNase- seq/FAIRE-seq/MNase-seq data. This is a modified version of r-spp to be used in conjunction with the phantompeakqualtools package.
r-phyloseq¶
- Homepage:
- Spack package:
- Versions:
- 1.20.0
- Build Dependencies:
- r, r-biocgenerics, r-reshape2, r-ape, r-cluster, r-ggplot2, r-multtest, r-igraph, r-foreach, r-ade4, r-vegan, r-biostrings, r-biobase, r-scales, r-biomformat, r-data-table, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r, r-biocgenerics, r-reshape2, r-ape, r-cluster, r-ggplot2, r-multtest, r-igraph, r-foreach, r-ade4, r-vegan, r-biostrings, r-biobase, r-scales, r-biomformat, r-data-table, r-plyr
- Description:
- phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
r-pkgconfig¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.
r-pkgmaker¶
- Homepage:
- Spack package:
- Versions:
- 0.22
- Build Dependencies:
- r-codetools, r-xtable, r-registry, r, r-stringr, r-digest
- Link Dependencies:
- r
- Run Dependencies:
- r-codetools, r-xtable, r-registry, r, r-stringr, r-digest
- Description:
- This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like NMF, RcppOctave, doRNG, and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.
r-plogr¶
- Homepage:
- Spack package:
- Versions:
- 0.1-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A simple header-only logging library for C++. Add 'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>' in your C++ modules to use it.
r-plotly¶
- Homepage:
- Spack package:
- Versions:
- 4.7.1, 4.7.0, 4.6.0, 4.5.6, 4.5.2
- Build Dependencies:
- r-hexbin, r-ggplot2, r-httr, r-data-table, r, r-dplyr, r-tidyr, r-base64enc, r-crosstalk, r-htmlwidgets, r-purrr, r-htmltools
- Link Dependencies:
- r
- Run Dependencies:
- r-hexbin, r-ggplot2, r-httr, r-data-table, r, r-dplyr, r-tidyr, r-base64enc, r-crosstalk, r-htmlwidgets, r-purrr, r-htmltools
- Description:
- Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.
r-plotrix¶
- Homepage:
- Spack package:
- Versions:
- 3.6-4, 3.6-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Lots of plots, various labeling, axis and color scaling functions.
r-pls¶
- Homepage:
- Spack package:
- Versions:
- 2.6-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
r-plyr¶
- Homepage:
- Spack package:
- Versions:
- 1.8.4
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.
r-pmcmr¶
- Homepage:
- Spack package:
- Versions:
- 4.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The Kruskal and Wallis one-way analysis of variance by ranks or van der Waerden's normal score test can be employed, if the data do not meet the assumptions for one-way ANOVA. Provided that significant differences were detected by the omnibus test, one may be interested in applying post-hoc tests for pairwise multiple comparisons (such as Nemenyi's test, Dunn's test, Conover's test, van der Waerden's test). Similarly, one-way ANOVA with repeated measures that is also referred to as ANOVA with unreplicated block design can also be conducted via the Friedman- Test or the Quade-test. The consequent post-hoc pairwise multiple comparison tests according to Nemenyi, Conover and Quade are also provided in this package. Finally Durbin's test for a two-way balanced incomplete block design (BIBD) is also given in this package.
r-png¶
- Homepage:
- Spack package:
- Versions:
- 0.1-7
- Build Dependencies:
- libpng, r
- Link Dependencies:
- libpng, r
- Run Dependencies:
- r
- Description:
- This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.
r-prabclus¶
- Homepage:
- Spack package:
- Versions:
- 2.2-6
- Build Dependencies:
- r-mclust, r
- Link Dependencies:
- r
- Run Dependencies:
- r-mclust, r
- Description:
- prabclus: Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data
r-praise¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.
r-preprocesscore¶
- Homepage:
- Spack package:
- Versions:
- 1.38.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A library of core preprocessing routines
r-prettyunits¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- r-magrittr, r-assertthat, r
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-assertthat, r
- Description:
- Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.
r-prodlim¶
- Homepage:
- Spack package:
- Versions:
- 1.5.9
- Build Dependencies:
- r-rcpp, r-survival, r, r-kernsmooth, r-lava
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r-survival, r, r-kernsmooth, r-lava
- Description:
- Product-Limit Estimation for Censored Event History Analysis. Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.
r-progress¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- r-r6, r-prettyunits, r
- Link Dependencies:
- r
- Run Dependencies:
- r-r6, r-prettyunits, r
- Description:
- Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.
r-protgenerics¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- S4 generic functions needed by Bioconductor proteomics packages.
r-proto¶
- Homepage:
- Spack package:
- Versions:
- 0.3-10
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An object oriented system using object-based, also called prototype- based, rather than class-based object oriented ideas.
r-proxy¶
- Homepage:
- Spack package:
- Versions:
- 0.4-19
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
r-pryr¶
- Homepage:
- Spack package:
- Versions:
- 0.1.2
- Build Dependencies:
- r-stringr, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-stringr, r-rcpp, r
- Description:
- Useful tools to pry back the covers of R and understand the language at a deeper level.
r-psych¶
- Homepage:
- Spack package:
- Versions:
- 1.7.8
- Build Dependencies:
- r-foreign, r-nlme, r-mnormt, r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-foreign, r-nlme, r-mnormt, r, r-lattice
- Description:
- A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <http://personality-project.org/r> web page.
r-ptw¶
- Homepage:
- Spack package:
- Versions:
- 1.9-12
- Build Dependencies:
- r-nloptr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-nloptr, r
- Description:
- Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.
r-purrr¶
- Homepage:
- Spack package:
- Versions:
- 0.2.4
- Build Dependencies:
- r-magrittr, r-rlang, r, r-tibble
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-rlang, r, r-tibble
- Description:
- A complete and consistent functional programming toolkit for R.
r-quadprog¶
- Homepage:
- Spack package:
- Versions:
- 1.5-5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package contains routines and documentation for solving quadratic programming problems.
r-quantmod¶
- Homepage:
- Spack package:
- Versions:
- 0.4-10, 0.4-5
- Build Dependencies:
- r-zoo, r-xts, r, r-curl, r-ttr
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-xts, r, r-curl, r-ttr
- Description:
- Specify, build, trade, and analyse quantitative financial trading strategies.
r-quantreg¶
- Homepage:
- Spack package:
- Versions:
- 5.29, 5.26
- Build Dependencies:
- r-sparsem, r, r-matrix, r-matrixmodels
- Link Dependencies:
- r
- Run Dependencies:
- r-sparsem, r, r-matrix, r-matrixmodels
- Description:
- Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.
r-quantro¶
- Homepage:
- Spack package:
- Versions:
- 1.10.0
- Build Dependencies:
- r-biobase, r-doparallel, r-iterators, r-ggplot2, r, r-minfi, r-foreach, r-rcolorbrewer
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-doparallel, r-iterators, r-ggplot2, r, r-minfi, r-foreach, r-rcolorbrewer
- Description:
- A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.
r-qvalue¶
- Homepage:
- Spack package:
- Versions:
- 2.8.0
- Build Dependencies:
- r-ggplot2, r-reshape2, r
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-reshape2, r
- Description:
- This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut- offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.
r-r6¶
- Homepage:
- Spack package:
- Versions:
- 2.2.2, 2.2.0, 2.1.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
r-randomforest¶
- Homepage:
- Spack package:
- Versions:
- 4.6-12
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Classification and regression based on a forest of trees using random inputs.
r-ranger¶
- Homepage:
- Spack package:
- Versions:
- 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0
- Build Dependencies:
- r-matrix, r-rcppeigen, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r-rcppeigen, r-rcpp, r
- Description:
- A fast implementation of Random Forests, particularly suited for high dimensional data.
r-rappdirs¶
- Homepage:
- Spack package:
- Versions:
- 0.3.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' to R.
r-raster¶
- Homepage:
- Spack package:
- Versions:
- 2.5-8
- Build Dependencies:
- r-sp, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-sp, r-rcpp, r
- Description:
- Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
r-rbgl¶
- Homepage:
- Spack package:
- Versions:
- 1.52.0
- Build Dependencies:
- r-graph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-graph, r
- Description:
- A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
r-rbokeh¶
- Homepage:
- Spack package:
- Versions:
- 0.5.0
- Build Dependencies:
- r-hexbin, r-pryr, r-ggplot2, r, r-magrittr, r-htmlwidgets, r-digest, r-maps, r-gistr, r-scales, r-jsonlite, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-hexbin, r-pryr, r-ggplot2, r, r-magrittr, r-htmlwidgets, r-digest, r-maps, r-gistr, r-scales, r-jsonlite, r-lazyeval
- Description:
- R interface for creating plots in Bokeh. Bokeh by Continuum Analytics.
r-rcolorbrewer¶
- Homepage:
- Spack package:
- Versions:
- 1.1-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org
r-rcpp¶
- Homepage:
- Spack package:
- Versions:
- 0.12.14, 0.12.13, 0.12.12, 0.12.11, 0.12.9, 0.12.6, 0.12.5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.
r-rcpparmadillo¶
- Homepage:
- Spack package:
- Versions:
- 0.8.100.1.0
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.
r-rcppcctz¶
- Homepage:
- Spack package:
- Versions:
- 0.2.3
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
r-rcppeigen¶
- Homepage:
- Spack package:
- Versions:
- 0.3.2.9.0, 0.3.2.8.1
- Build Dependencies:
- r-matrix, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r-rcpp, r
- Description:
- R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library (currently version 3.2.8). Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
r-rcppprogress¶
- Homepage:
- Spack package:
- Versions:
- 0.3, 0.2.1, 0.2, 0.1
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.
r-rcurl¶
- Homepage:
- Spack package:
- Versions:
- 1.95-4.8
- Build Dependencies:
- curl, r-bitops, r
- Link Dependencies:
- curl, r
- Run Dependencies:
- r-bitops, r
- Description:
- A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
r-rda¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.
r-readr¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- r-bh, r, r-tibble, r-r6, r-rcpp, r-hms
- Link Dependencies:
- r
- Run Dependencies:
- r-bh, r, r-tibble, r-r6, r-rcpp, r-hms
- Description:
- The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
r-readxl¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- r-tibble, r, r-rcpp, r-cellranger
- Link Dependencies:
- r
- Run Dependencies:
- r-tibble, r, r-rcpp, r-cellranger
- Description:
- Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://sourceforge.net/projects/libxls/> and '.xlsx' via the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.
r-registry¶
- Homepage:
- Spack package:
- Versions:
- 0.3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides a generic infrastructure for creating and using registries.
r-rematch¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- r-covr, r-testthat, r
- Link Dependencies:
- r
- Run Dependencies:
- r-covr, r-testthat, r
- Description:
- A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.
r-reordercluster¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- r-gplots, r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gplots, r-rcpp, r
- Description:
- Tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.
r-reportingtools¶
- Homepage:
- Spack package:
- Versions:
- 2.16.0
- Build Dependencies:
- r-annotationdbi, r-biocgenerics, r-iranges, r-gseabase, r-ggplot2, r, r-edger, r-ggbio, r-hwriter, r-limma, r-lattice, r-category, r-biobase, r-annotate, r-gostats, r-knitr, r-deseq2, r-pfam-db, r-xml, r-utils
- Link Dependencies:
- r
- Run Dependencies:
- r-annotationdbi, r-biocgenerics, r-iranges, r-gseabase, r-ggplot2, r, r-edger, r-ggbio, r-hwriter, r-limma, r-lattice, r-category, r-biobase, r-annotate, r-gostats, r-knitr, r-deseq2, r-pfam-db, r-xml, r-utils
- Description:
- The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.
r-repr¶
- Homepage:
- Spack package:
- Versions:
- 0.9
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- String and binary representations of objects for several formats and mime types.
r-reprex¶
- Homepage:
- Spack package:
- Versions:
- 0.1.1
- Build Dependencies:
- r-callr, r, r-clipr, r-rmarkdown, r-whisker, r-knitr
- Link Dependencies:
- r
- Run Dependencies:
- r-callr, r, r-clipr, r-rmarkdown, r-whisker, r-knitr
- Description:
- Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <http://stackoverflow.com> and <https://github.com>, or in email. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.
r-reshape¶
- Homepage:
- Spack package:
- Versions:
- 0.8.7
- Build Dependencies:
- r, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r, r-plyr
- Description:
- Flexibly restructure and aggregate data using just two functions: melt and cast.
r-reshape2¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2, 1.4.1
- Build Dependencies:
- r-stringr, r, r-rcpp, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-stringr, r, r-rcpp, r-plyr
- Description:
- Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).
r-rex¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- r-magrittr, r, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r, r-lazyeval
- Description:
- A friendly interface for the construction of regular expressions.
r-rgdal¶
- Homepage:
- Spack package:
- Versions:
- 1.2-16
- Build Dependencies:
- r-sp, gdal, proj, r
- Link Dependencies:
- gdal, proj, r
- Run Dependencies:
- r-sp, r
- Description:
- Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.6.3) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
r-rgeos¶
- Homepage:
- Spack package:
- Versions:
- 0.3-26
- Build Dependencies:
- r-sp, geos, r
- Link Dependencies:
- geos, r
- Run Dependencies:
- r-sp, r
- Description:
- Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.
r-rgl¶
- Homepage:
- Spack package:
- Versions:
- 0.98.1
- Build Dependencies:
- r-magrittr, libx11, r, r-htmlwidgets, r-htmltools, r-shiny, r-knitr, r-jsonlite
- Link Dependencies:
- libpng, zlib, libx11, r, freetype, mesa-glu, mesa
- Run Dependencies:
- r-magrittr, r, r-htmlwidgets, r-htmltools, r-shiny, r-knitr, r-jsonlite
- Description:
- Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
r-rgooglemaps¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0.7
- Build Dependencies:
- r-rjsonio, r-png, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rjsonio, r-png, r
- Description:
- This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.
r-rgraphviz¶
- Homepage:
- Spack package:
- Versions:
- 2.20.0
- Build Dependencies:
- r-graph, r
- Link Dependencies:
- r
- Run Dependencies:
- r-graph, r
- Description:
- Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.
r-rhdf5¶
- Homepage:
- Spack package:
- Versions:
- 2.20.0
- Build Dependencies:
- r-zlibbioc, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zlibbioc, r
- Description:
- This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
r-rhtslib¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- autoconf, r-zlibbioc, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zlibbioc, r
- Description:
- This package provides version 1.1 of the 'HTSlib' C library for high- throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").
r-rinside¶
- Homepage:
- Spack package:
- Versions:
- 0.2.13
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- C++ classes to embed R in C++ applications The 'RInside' packages makes it easier to have "R inside" your C++ application by providing a C++ wrapperclass providing the R interpreter. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the eight subdirectories of the examples/ directory of the installed package: standard, mpi (for parallel computing) qt (showing how to embed 'RInside' inside a Qt GUI application), wt (showing how to build a "web- application" using the Wt toolkit), armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with 'RcppEigen'). The example use GNUmakefile(s) with GNU extensions, so a GNU make is required (and will use the GNUmakefile automatically). Doxygen-generated documentation of the C++ classes is available at the 'RInside' website as well.
r-rjags¶
- Homepage:
- Spack package:
- Versions:
- 4-6
- Build Dependencies:
- r-coda, r
- Link Dependencies:
- jags, r
- Run Dependencies:
- r-coda, r
- Description:
- Interface to the JAGS MCMC library. Usage: $ spack load r-rjags
r-rjava¶
- Homepage:
- Spack package:
- Versions:
- 0.9-8
- Build Dependencies:
- java, r
- Link Dependencies:
- java, r
- Run Dependencies:
- r
- Description:
- Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
r-rjson¶
- Homepage:
- Spack package:
- Versions:
- 0.2.15
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Converts R object into JSON objects and vice-versa.
r-rjsonio¶
- Homepage:
- Spack package:
- Versions:
- 1.3-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.
r-rlang¶
- Homepage:
- Spack package:
- Versions:
- 0.1.2, 0.1.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
r-rmarkdown¶
- Homepage:
- Spack package:
- Versions:
- 1.7, 1.0
- Build Dependencies:
- r-base64enc, r-yaml, r, r-rprojroot, r-htmltools, r-stringr, r-evaluate, r-knitr, r-jsonlite, r-mime
- Link Dependencies:
- r
- Run Dependencies:
- r-base64enc, r-yaml, r, r-rprojroot, r-htmltools, r-stringr, r-evaluate, r-knitr, r-jsonlite, r-mime
- Description:
- Convert R Markdown documents into a variety of formats.
r-rminer¶
- Homepage:
- Spack package:
- Versions:
- 1.4.2
- Build Dependencies:
- r-pls, r-glmnet, r-kknn, r-mda, r-kernlab, r-lattice, r-adabag, r, r-plotrix, r-xgboost, r-randomforest, r-rpart, r-cubist, r-e1071, r-nnet, r-mass, r-party
- Link Dependencies:
- r
- Run Dependencies:
- r-pls, r-glmnet, r-kknn, r-mda, r-kernlab, r-lattice, r-adabag, r, r-plotrix, r-xgboost, r-randomforest, r-rpart, r-cubist, r-e1071, r-nnet, r-mass, r-party
- Description:
- Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions.
r-rmpfr¶
- Homepage:
- Spack package:
- Versions:
- 0.6-1
- Build Dependencies:
- mpfr, r, r-gmp
- Link Dependencies:
- r, mpfr
- Run Dependencies:
- r, r-gmp
- Description:
- Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, Rmpfr interfaces to the LGPL'ed MPFR (Multiple Precision Floating- Point Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library.
r-rmpi¶
- Homepage:
- Spack package:
- Versions:
- 0.6-6
- Build Dependencies:
- r, mpi
- Link Dependencies:
- r, mpi
- Run Dependencies:
- r
- Description:
- An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.
r-rmysql¶
- Homepage:
- Spack package:
- Versions:
- 0.10.9
- Build Dependencies:
- mariadb, r-dbi, r
- Link Dependencies:
- mariadb, r
- Run Dependencies:
- r-dbi, r
- Description:
- Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
r-rngtools¶
- Homepage:
- Spack package:
- Versions:
- 1.2.4
- Build Dependencies:
- r-stringr, r, r-digest, r-pkgmaker
- Link Dependencies:
- r
- Run Dependencies:
- r-stringr, r, r-digest, r-pkgmaker
- Description:
- This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.
r-robustbase¶
- Homepage:
- Spack package:
- Versions:
- 0.92-7
- Build Dependencies:
- r-deoptimr, r
- Link Dependencies:
- r
- Run Dependencies:
- r-deoptimr, r
- Description:
- "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
r-rocr¶
- Homepage:
- Spack package:
- Versions:
- 1.0-7
- Build Dependencies:
- r-gplots, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gplots, r
- Description:
- ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross- validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.
r-rodbc¶
- Homepage:
- Spack package:
- Versions:
- 1.3-13
- Build Dependencies:
- unixodbc, r
- Link Dependencies:
- unixodbc, r
- Run Dependencies:
- r
- Description:
- An ODBC database interface.
r-roxygen2¶
- Homepage:
- Spack package:
- Versions:
- 5.0.1
- Build Dependencies:
- r-rcpp, r-digest, r, r-brew, r-stringr, r-stringi
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r-digest, r, r-brew, r-stringr, r-stringi
- Description:
- A 'Doxygen'-like in-source documentation system for Rd, collation, and 'NAMESPACE' files.
r-rpart¶
- Homepage:
- Spack package:
- Versions:
- 4.1-11, 4.1-10
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Recursive partitioning for classification, regression and survival trees.
r-rpart-plot¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0
- Build Dependencies:
- r-rpart, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rpart, r
- Description:
- Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
r-rpostgresql¶
- Homepage:
- Spack package:
- Versions:
- 0.4-1
- Build Dependencies:
- postgresql, r-dbi, r
- Link Dependencies:
- postgresql, r
- Run Dependencies:
- r-dbi, r
- Description:
- Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. In order to build and install this package from source, PostgreSQL itself must be present your system to provide PostgreSQL functionality via its libraries and header files. These files are provided as postgresql-devel package under some Linux distributions. On Microsoft Windows system the attached libpq library source will be used. A wiki and issue tracking system for the package are available at Google Code at https://code.google.com/p/rpostgresql/.
r-rprojroot¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- r-backports, r
- Link Dependencies:
- r
- Run Dependencies:
- r-backports, r
- Description:
- Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.
r-rsamtools¶
- Homepage:
- Spack package:
- Versions:
- 1.28.0
- Build Dependencies:
- r, r-biostrings, r-xvector, r-genomicranges, r-biocgenerics, r-s4vectors, r-biocparallel, r-genomeinfodb, r-iranges, r-bitops, r-zlibbioc
- Link Dependencies:
- r
- Run Dependencies:
- r, r-biostrings, r-xvector, r-genomicranges, r-biocgenerics, r-s4vectors, r-biocparallel, r-genomeinfodb, r-iranges, r-bitops, r-zlibbioc
- Description:
- This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
r-rsnns¶
- Homepage:
- Spack package:
- Versions:
- 0.4-7
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.
r-rsqlite¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- r-pkgconfig, r-blob, r-dbi, r, r-plogr, r-bit64, r-rcpp, r-bh, r-memoise
- Link Dependencies:
- r
- Run Dependencies:
- r-pkgconfig, r-blob, r-dbi, r, r-plogr, r-bit64, r-rcpp, r-bh, r-memoise
- Description:
- This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.
r-rstan¶
- Homepage:
- Spack package:
- Versions:
- 2.10.1
- Build Dependencies:
- r-ggplot2, r-rcppeigen, r-inline, r-gridextra, r, r-rcpp, r-bh, r-stanheaders
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-rcppeigen, r-inline, r-gridextra, r, r-rcpp, r-bh, r-stanheaders
- Description:
- User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
r-rstudioapi¶
- Homepage:
- Spack package:
- Versions:
- 0.6, 0.5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Access the RStudio API (if available) and provide informative error messages when it's not.
r-rtracklayer¶
- Homepage:
- Spack package:
- Versions:
- 1.36.6
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r-genomeinfodb, r, r-xml, r-rsamtools, r-iranges, r-biostrings, r-zlibbioc, r-s4vectors, r-rcurl, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r-genomeinfodb, r, r-xml, r-rsamtools, r-iranges, r-biostrings, r-zlibbioc, r-s4vectors, r-rcurl, r-xvector
- Description:
- Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
r-rtsne¶
- Homepage:
- Spack package:
- Versions:
- 0.13, 0.11, 0.10
- Build Dependencies:
- r-rcpp, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rcpp, r
- Description:
- An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation.
r-rvcheck¶
- Homepage:
- Spack package:
- Versions:
- 0.0.9
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
r-rvest¶
- Homepage:
- Spack package:
- Versions:
- 0.3.2
- Build Dependencies:
- r, r-selectr, r-xml2, r-httr, r-magrittr
- Link Dependencies:
- r
- Run Dependencies:
- r, r-selectr, r-xml2, r-httr, r-magrittr
- Description:
- Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.
r-rzmq¶
- Homepage:
- Spack package:
- Versions:
- 0.7.7
- Build Dependencies:
- zeromq, r
- Link Dependencies:
- zeromq, r
- Run Dependencies:
- r
- Description:
- Interface to the ZeroMQ lightweight messaging kernel.
r-s4vectors¶
- Homepage:
- Spack package:
- Versions:
- 0.14.7
- Build Dependencies:
- r-biocgenerics, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r
- Description:
- The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
r-samr¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- r-matrixstats, r, r-impute
- Link Dependencies:
- r
- Run Dependencies:
- r-matrixstats, r, r-impute
- Description:
- Significance Analysis of Microarrays.
r-sandwich¶
- Homepage:
- Spack package:
- Versions:
- 2.3-4
- Build Dependencies:
- r-zoo, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r
- Description:
- Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.
r-scales¶
- Homepage:
- Spack package:
- Versions:
- 0.5.0, 0.4.1, 0.4.0
- Build Dependencies:
- r-labeling, r-viridislite, r, r-munsell, r-r6, r-dichromat, r-rcpp, r-rcolorbrewer, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-labeling, r-viridislite, r, r-munsell, r-r6, r-dichromat, r-rcpp, r-rcolorbrewer, r-plyr
- Description:
- Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
r-scatterplot3d¶
- Homepage:
- Spack package:
- Versions:
- 0.3-40
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- scatterplot3d: 3D Scatter Plot
r-sdmtools¶
- Homepage:
- Spack package:
- Versions:
- 1.1-221, 1.1-20, 1.1-13, 1.1-12, 1.1-11
- Build Dependencies:
- r-utils, r
- Link Dependencies:
- r
- Run Dependencies:
- r-utils, r
- Description:
- Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises.
r-segmented¶
- Homepage:
- Spack package:
- Versions:
- 0.5-2.2, 0.5-1.4
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Given a regression model, segmented 'updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
r-selectr¶
- Homepage:
- Spack package:
- Versions:
- 0.3-1
- Build Dependencies:
- r-testthat, r, r-stringr, r-xml, r-xml2
- Link Dependencies:
- r
- Run Dependencies:
- r-testthat, r, r-stringr, r-xml, r-xml2
- Description:
- Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://pythonhosted.org/cssselect/>).
r-seqinr¶
- Homepage:
- Spack package:
- Versions:
- 3.4-5, 3.3-6
- Build Dependencies:
- r-ade4, r-segmented, zlib, r
- Link Dependencies:
- zlib, r
- Run Dependencies:
- r-segmented, r-ade4, r
- Description:
- Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.
r-seurat¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 2.0.1
- Build Dependencies:
- r-ggplot2, r-nmf, r-ape, r, r-gplots, r-dtw, r-fnn, r-lars, r-tsne, r-cowplot, r-pbapply, r-rcppprogress, r-glue, r-rocr, r-caret, r-fpc, r-pkgconfig, r-reshape2, r-hmisc, r-ica, r-irlba, r-vgam, r-plotly, r-ranger, r-ggjoy, r-diffusionmap, r-sdmtools, r-gdata, r-rtsne, r-gridextra, r-plogr, r-tclust, r-igraph, r-mixtools, r-tidyr
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-nmf, r-ape, r, r-gplots, r-dtw, r-fnn, r-lars, r-tsne, r-cowplot, r-pbapply, r-rcppprogress, r-glue, r-rocr, r-caret, r-fpc, r-pkgconfig, r-reshape2, r-hmisc, r-ica, r-irlba, r-vgam, r-plotly, r-ranger, r-ggjoy, r-diffusionmap, r-sdmtools, r-gdata, r-rtsne, r-gridextra, r-plogr, r-tclust, r-igraph, r-mixtools, r-tidyr
- Description:
- Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
r-sfsmisc¶
- Homepage:
- Spack package:
- Versions:
- 1.1-0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, quite a few related to graphics; some were ported from S-plus.
r-shape¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3, 1.4.2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...
r-shiny¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5, 0.13.2
- Build Dependencies:
- r-digest, r-xtable, r, r-httpuv, r-mime, r-htmltools, r-r6, r-jsonlite, r-sourcetools
- Link Dependencies:
- r
- Run Dependencies:
- r-digest, r-xtable, r, r-httpuv, r-mime, r-htmltools, r-r6, r-jsonlite, r-sourcetools
- Description:
- Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
r-shortread¶
- Homepage:
- Spack package:
- Versions:
- 1.34.2
- Build Dependencies:
- r-genomicalignments, r-biocgenerics, r-hwriter, r, r-biocparallel, r-genomeinfodb, r-iranges, r-biobase, r-latticeextra, r-zlibbioc, r-s4vectors, r-lattice, r-rsamtools, r-genomicranges, r-biostrings
- Link Dependencies:
- r
- Run Dependencies:
- r-genomicalignments, r-biocgenerics, r-hwriter, r, r-biocparallel, r-genomeinfodb, r-iranges, r-biobase, r-latticeextra, r-zlibbioc, r-s4vectors, r-lattice, r-rsamtools, r-genomicranges, r-biostrings
- Description:
- This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
r-siggenes¶
- Homepage:
- Spack package:
- Versions:
- 1.50.0
- Build Dependencies:
- r-biobase, r, r-multtest
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r, r-multtest
- Description:
- Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
r-simpleaffy¶
- Homepage:
- Spack package:
- Versions:
- 2.52.0
- Build Dependencies:
- r-biocgenerics, r-genefilter, r-biobase, r-gcrma, r-affy, r
- Link Dependencies:
- r
- Run Dependencies:
- r-biocgenerics, r-genefilter, r-biobase, r-gcrma, r-affy, r
- Description:
- Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...
r-sn¶
- Homepage:
- Spack package:
- Versions:
- 1.5-0, 1.4-0, 1.3-0, 1.2-4, 1.2-3
- Build Dependencies:
- r-numderiv, r-mnormt, r
- Link Dependencies:
- r
- Run Dependencies:
- r-numderiv, r-mnormt, r
- Description:
- Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.
r-snow¶
- Homepage:
- Spack package:
- Versions:
- 0.4-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r-rmpi, r
- Description:
- Support for simple parallel computing in R.
r-snprelate¶
- Homepage:
- Spack package:
- Versions:
- 1.12.2
- Build Dependencies:
- r-gdsfmt, r
- Link Dependencies:
- r
- Run Dependencies:
- r-gdsfmt, r
- Description:
- Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.
r-som¶
- Homepage:
- Spack package:
- Versions:
- 0.3-5.1, 0.3-5, 0.3-4, 0.3-3, 0.3-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Self-Organizing Map (with application in gene clustering).
r-somaticsignatures¶
- Homepage:
- Spack package:
- Versions:
- 2.12.1
- Build Dependencies:
- r-ggplot2, r-nmf, r-biostrings, r-ggbio, r-iranges, r-variantannotation, r-genomeinfodb, r, r-reshape2, r-biobase, r-genomicranges, r-s4vectors, r-pcamethods, r-proxy
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-nmf, r-biostrings, r-ggbio, r-iranges, r-variantannotation, r-genomeinfodb, r, r-reshape2, r-biobase, r-genomicranges, r-s4vectors, r-pcamethods, r-proxy
- Description:
- The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.
r-sourcetools¶
- Homepage:
- Spack package:
- Versions:
- 0.1.6, 0.1.5
- Build Dependencies:
- r-testthat, r
- Link Dependencies:
- r
- Run Dependencies:
- r-testthat, r
- Description:
- Tools for Reading, Tokenizing and Parsing R Code.
r-sp¶
- Homepage:
- Spack package:
- Versions:
- 1.2-3
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
r-sparsem¶
- Homepage:
- Spack package:
- Versions:
- 1.74, 1.7
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.
r-spdep¶
- Homepage:
- Spack package:
- Versions:
- 0.6-13
- Build Dependencies:
- r-gmodels, r-sp, r-coda, r-expm, r, r-learnbayes, r-deldir
- Link Dependencies:
- r
- Run Dependencies:
- r-gmodels, r-sp, r-coda, r-expm, r, r-learnbayes, r-deldir
- Description:
- A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and AssunasReis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.
r-speedglm¶
- Homepage:
- Spack package:
- Versions:
- 0.3-2
- Build Dependencies:
- r-matrix, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r-mass, r
- Description:
- Fitting linear models and generalized linear models to large data sets by updating algorithms.
r-sqldf¶
- Homepage:
- Spack package:
- Versions:
- 0.4-11
- Build Dependencies:
- r-rsqlite, r-chron, r-dbi, r-proto, r, r-gsubfn
- Link Dependencies:
- r
- Run Dependencies:
- r-rsqlite, r-chron, r-dbi, r-proto, r, r-gsubfn
- Description:
- The sqldf() function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. sqldf() transparently sets up a database, imports the data frames into that database, performs the SQL select or other statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf() or read.csv.sql() functions can also be used to read filtered files into R even if the original files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.
r-stanheaders¶
- Homepage:
- Spack package:
- Versions:
- 2.10.0-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
r-statmod¶
- Homepage:
- Spack package:
- Versions:
- 1.4.30
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
r-statnet-common¶
- Homepage:
- Spack package:
- Versions:
- 3.3.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
r-stringi¶
- Homepage:
- Spack package:
- Versions:
- 1.1.5, 1.1.3, 1.1.2, 1.1.1
- Build Dependencies:
- icu4c, r
- Link Dependencies:
- icu4c, r
- Run Dependencies:
- r
- Description:
- Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.
r-stringr¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0, 1.1.0, 1.0.0
- Build Dependencies:
- r-stringi, r, r-magrittr
- Link Dependencies:
- r
- Run Dependencies:
- r-stringi, r, r-magrittr
- Description:
- A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
r-strucchange¶
- Homepage:
- Spack package:
- Versions:
- 1.5-1
- Build Dependencies:
- r-zoo, r-sandwich, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-sandwich, r
- Description:
- Testing, monitoring and dating structural changes in (linear) regression models.
r-subplex¶
- Homepage:
- Spack package:
- Versions:
- 1.4-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Unconstrained Optimization using the Subplex Algorithm
r-summarizedexperiment¶
- Homepage:
- Spack package:
- Versions:
- 1.6.5
- Build Dependencies:
- r-biobase, r-matrix, r-genomicranges, r, r-s4vectors, r-genomeinfodb, r-iranges, r-delayedarray
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-matrix, r-genomicranges, r, r-s4vectors, r-genomeinfodb, r-iranges, r-delayedarray
- Description:
- The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
r-survey¶
- Homepage:
- Spack package:
- Versions:
- 3.30-3
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
r-survival¶
- Homepage:
- Spack package:
- Versions:
- 2.41-3, 2.40-1, 2.39-5
- Build Dependencies:
- r-matrix, r
- Link Dependencies:
- r
- Run Dependencies:
- r-matrix, r
- Description:
- Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
r-sva¶
- Homepage:
- Spack package:
- Versions:
- 3.24.4
- Build Dependencies:
- r-genefilter, r-mgcv, r, r-matrixstats, r-limma, r-biocparallel
- Link Dependencies:
- r
- Run Dependencies:
- r-genefilter, r-mgcv, r, r-matrixstats, r-limma, r-biocparallel
- Description:
- Surrogate Variable Analysis.
r-tarifx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- r-reshape2, r, r-plyr
- Link Dependencies:
- r
- Run Dependencies:
- r-reshape2, r, r-plyr
- Description:
- A collection of various utility and convenience functions.
r-tclust¶
- Homepage:
- Spack package:
- Versions:
- 1.3-1, 1.2-7, 1.2-3, 1.1-03, 1.1-02
- Build Dependencies:
- r, r-cluster, r-mclust, r-mvtnorm, r-sn
- Link Dependencies:
- r
- Run Dependencies:
- r, r-cluster, r-mclust, r-mvtnorm, r-sn
- Description:
- Provides functions for robust trimmed clustering.
r-tensora¶
- Homepage:
- Spack package:
- Versions:
- 0.36
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- The package provides convenience functions for advance linear algebra with tensors and computation with datasets of tensors on a higher level abstraction.
r-testit¶
- Homepage:
- Spack package:
- Versions:
- 0.7, 0.5
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.
r-testthat¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- r-magrittr, r-digest, r, r-r6, r-praise, r-crayon
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-digest, r, r-r6, r-praise, r-crayon
- Description:
- A unit testing system designed to be fun, flexible and easy to set up.
r-th-data¶
- Homepage:
- Spack package:
- Versions:
- 1.0-8, 1.0-7
- Build Dependencies:
- r-survival, r-mass, r
- Link Dependencies:
- r
- Run Dependencies:
- r-survival, r-mass, r
- Description:
- Contains data sets used in other packages Torsten Hothorn maintains.
r-threejs¶
- Homepage:
- Spack package:
- Versions:
- 0.2.2
- Build Dependencies:
- r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite, r
- Link Dependencies:
- r
- Run Dependencies:
- r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite, r
- Description:
- Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ("http://threejs.org").
r-tibble¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4, 1.2, 1.1
- Build Dependencies:
- r, r-rlang, r-rcpp, r-assertthat, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r, r-rlang, r-rcpp, r-assertthat, r-lazyeval
- Description:
- Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.
r-tidycensus¶
- Homepage:
- Spack package:
- Versions:
- 0.3.1
- Build Dependencies:
- r-rvest, r-tidyr, r-httr, r-tigris, r-xml2, r-dplyr, r-sf, r, r-units, r-purrr, r-rappdirs, r-readr, r-stringr, r-jsonlite
- Link Dependencies:
- r
- Run Dependencies:
- r-rvest, r-tidyr, r-httr, r-tigris, r-xml2, r-dplyr, r-sf, r, r-units, r-purrr, r-rappdirs, r-readr, r-stringr, r-jsonlite
- Description:
- An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many geographies.
r-tidyr¶
- Homepage:
- Spack package:
- Versions:
- 0.5.1
- Build Dependencies:
- r-magrittr, r, r-tibble, r-stringi, r-rcpp, r-dplyr, r-lazyeval
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r, r-tibble, r-stringi, r-rcpp, r-dplyr, r-lazyeval
- Description:
- An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.
r-tiff¶
- Homepage:
- Spack package:
- Versions:
- 0.1-5
- Build Dependencies:
- libjpeg, libtiff, r
- Link Dependencies:
- libjpeg, libtiff, r
- Run Dependencies:
- r
- Description:
- This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.
r-tigris¶
- Homepage:
- Spack package:
- Versions:
- 0.5.3
- Build Dependencies:
- r-magrittr, r-httr, r-maptools, r, r-sf, r-rappdirs, r-rgeos, r-sp, r-uuid, r-stringr, r-dplyr, r-rgdal
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-httr, r-maptools, r, r-sf, r-rappdirs, r-rgeos, r-sp, r-uuid, r-stringr, r-dplyr, r-rgdal
- Description:
- Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.
r-timedate¶
- Homepage:
- Spack package:
- Versions:
- 3012.100
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.
r-topgo¶
- Homepage:
- Spack package:
- Versions:
- 2.28.0
- Build Dependencies:
- r-biobase, r-dbi, r, r-sparsem, r-matrixstats, r-biocgenerics, r-annotationdbi, r-graph, r-go-db, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-dbi, r, r-sparsem, r-matrixstats, r-biocgenerics, r-annotationdbi, r-graph, r-go-db, r-lattice
- Description:
- topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
r-trimcluster¶
- Homepage:
- Spack package:
- Versions:
- 0.1-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- trimcluster: Cluster analysis with trimming
r-trust¶
- Homepage:
- Spack package:
- Versions:
- 0.1-7
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.
r-tseries¶
- Homepage:
- Spack package:
- Versions:
- 0.10-42
- Build Dependencies:
- r-zoo, r-quadprog, r-quantmod, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-quadprog, r-quantmod, r
- Description:
- Time series analysis and computational finance.
r-tsne¶
- Homepage:
- Spack package:
- Versions:
- 0.1-3, 0.1-2, 0.1-1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A "pure R" implementation of the t-SNE algorithm.
r-ttr¶
- Homepage:
- Spack package:
- Versions:
- 0.23-1
- Build Dependencies:
- r-zoo, r-xts, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r-xts, r
- Description:
- Functions and data to construct technical trading rules with R.
r-udunits2¶
- Homepage:
- Spack package:
- Versions:
- 0.13
- Build Dependencies:
- udunits2, r
- Link Dependencies:
- udunits2, r
- Run Dependencies:
- r
- Description:
- Provides simple bindings to Unidata's udunits library.
r-units¶
- Homepage:
- Spack package:
- Versions:
- 0.4-6
- Build Dependencies:
- r-udunits2, r
- Link Dependencies:
- r
- Run Dependencies:
- r-udunits2, r
- Description:
- Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion.
r-utils¶
- Homepage:
- Spack package:
- Versions:
- 2.5.0
- Build Dependencies:
- r-oo, r
- Link Dependencies:
- r
- Run Dependencies:
- r-oo, r
- Description:
- Utility functions useful when programming and developing R packages.
r-uuid¶
- Homepage:
- Spack package:
- Versions:
- 0.1-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Tools for generating and handling of UUIDs (Universally Unique Identifiers).
r-variantannotation¶
- Homepage:
- Spack package:
- Versions:
- 1.22.3
- Build Dependencies:
- r, r-biocgenerics, r-dbi, r-genomeinfodb, r-annotationdbi, r-rsamtools, r-iranges, r-summarizedexperiment, r-biobase, r-genomicranges, r-genomicfeatures, r-s4vectors, r-rtracklayer, r-bsgenome, r-biostrings, r-zlibbioc, r-xvector
- Link Dependencies:
- r
- Run Dependencies:
- r, r-biocgenerics, r-dbi, r-genomeinfodb, r-annotationdbi, r-rsamtools, r-iranges, r-summarizedexperiment, r-biobase, r-genomicranges, r-genomicfeatures, r-s4vectors, r-rtracklayer, r-bsgenome, r-biostrings, r-zlibbioc, r-xvector
- Description:
- Annotate variants, compute amino acid coding changes, predict coding outcomes.
r-varselrf¶
- Homepage:
- Spack package:
- Versions:
- 0.7-8
- Build Dependencies:
- r, r-randomforest
- Link Dependencies:
- r
- Run Dependencies:
- r, r-randomforest
- Description:
- Variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree plots; for the selection of large, potentially highly-correlated variables) . Main applications in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications).
r-vcd¶
- Homepage:
- Spack package:
- Versions:
- 1.4-1
- Build Dependencies:
- r-colorspace, r, r-mass, r-lmtest
- Link Dependencies:
- r
- Run Dependencies:
- r-colorspace, r, r-mass, r-lmtest
- Description:
- Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).
r-vegan¶
- Homepage:
- Spack package:
- Versions:
- 2.4-3
- Build Dependencies:
- r-permute, r
- Link Dependencies:
- r
- Run Dependencies:
- r-permute, r
- Description:
- Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
r-vgam¶
- Homepage:
- Spack package:
- Versions:
- 1.0-4, 1.0-3, 1.0-2, 1.0-1, 1.0-0
- Build Dependencies:
- r-mass, r-mgcv, r
- Link Dependencies:
- r
- Run Dependencies:
- r-mass, r-mgcv, r
- Description:
- An implementation of about 6 major classes of statistical regression models.
r-viridis¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- r-ggplot2, r-viridislite, r-gridextra, r
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-viridislite, r-gridextra, r
- Description:
- viridis: Default Color Maps from 'matplotlib'
r-viridislite¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- viridisLite: Default Color Maps from 'matplotlib' (Lite Version)
r-visnetwork¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- r-htmlwidgets, r-magrittr, r-htmltools, r-jsonlite, r
- Link Dependencies:
- r
- Run Dependencies:
- r-htmlwidgets, r-magrittr, r-htmltools, r-jsonlite, r
- Description:
- Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
r-vsn¶
- Homepage:
- Spack package:
- Versions:
- 3.44.0
- Build Dependencies:
- r-hexbin, r-biobase, r-affy, r-ggplot2, r, r-limma, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r-hexbin, r-biobase, r-affy, r-ggplot2, r, r-limma, r-lattice
- Description:
- The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
r-whisker¶
- Homepage:
- Spack package:
- Versions:
- 0.3-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- logicless templating, reuse templates in many programming languages including R
r-withr¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2, 1.0.1
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
r-xde¶
- Homepage:
- Spack package:
- Versions:
- 2.22.0
- Build Dependencies:
- r-biobase, r-genefilter, r-gtools, r-mergemaid, r-biocgenerics, r, r-mvtnorm
- Link Dependencies:
- r
- Run Dependencies:
- r-biobase, r-genefilter, r-gtools, r-mergemaid, r-biocgenerics, r, r-mvtnorm
- Description:
- Multi-level model for cross-study detection of differential gene expression.
r-xgboost¶
- Homepage:
- Spack package:
- Versions:
- 0.6-4, 0.4-4
- Build Dependencies:
- r-magrittr, r-matrix, r, r-stringi, r-stringr, r-data-table
- Link Dependencies:
- r
- Run Dependencies:
- r-magrittr, r-matrix, r, r-stringi, r-stringr, r-data-table
- Description:
- Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.
r-xlconnect¶
- Homepage:
- Spack package:
- Versions:
- 0.2-12, 0.2-11
- Build Dependencies:
- r-xlconnectjars, r-rjava, r
- Link Dependencies:
- r
- Run Dependencies:
- r-xlconnectjars, r-rjava, r
- Description:
- Provides comprehensive functionality to read, write and format Excel data.
r-xlconnectjars¶
- Homepage:
- Spack package:
- Versions:
- 0.2-12, 0.2-9
- Build Dependencies:
- r-rjava, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rjava, r
- Description:
- Provides external JAR dependencies for the XLConnect package.
r-xlsx¶
- Homepage:
- Spack package:
- Versions:
- 0.5.7
- Build Dependencies:
- r-xlsxjars, r-rjava, r
- Link Dependencies:
- r
- Run Dependencies:
- r-xlsxjars, r-rjava, r
- Description:
- Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
r-xlsxjars¶
- Homepage:
- Spack package:
- Versions:
- 0.6.1
- Build Dependencies:
- r-rjava, r
- Link Dependencies:
- r
- Run Dependencies:
- r-rjava, r
- Description:
- The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.
r-xmapbridge¶
- Homepage:
- Spack package:
- Versions:
- 1.34.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.
r-xml¶
- Homepage:
- Spack package:
- Versions:
- 3.98-1.9, 3.98-1.5, 3.98-1.4
- Build Dependencies:
- r, libxml2
- Link Dependencies:
- r, libxml2
- Run Dependencies:
- r
- Description:
- Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
r-xml2¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- r-bh, r, r-rcpp, libxml2
- Link Dependencies:
- r, libxml2
- Run Dependencies:
- r-bh, r-rcpp, r
- Description:
- Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
r-xtable¶
- Homepage:
- Spack package:
- Versions:
- 1.8-2
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- Coerce data to LaTeX and HTML tables.
r-xts¶
- Homepage:
- Spack package:
- Versions:
- 0.9-7
- Build Dependencies:
- r-zoo, r
- Link Dependencies:
- r
- Run Dependencies:
- r-zoo, r
- Description:
- Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
r-xvector¶
- Homepage:
- Spack package:
- Versions:
- 0.16.0
- Build Dependencies:
- r-s4vectors, r-biocgenerics, r-iranges, r-zlibbioc, r
- Link Dependencies:
- r
- Run Dependencies:
- r-s4vectors, r-biocgenerics, r-iranges, r-zlibbioc, r
- Description:
- Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).
r-yaml¶
- Homepage:
- Spack package:
- Versions:
- 2.1.14, 2.1.13
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.
r-yapsa¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r-ggplot2, r-reshape2, r-complexheatmap, r-genomeinfodb, r-variantannotation, r, r-getoptlong, r-keggrest, r-corrplot, r-gtrellis, r-dendextend, r-genomicranges, r-gridextra, r-somaticsignatures, r-pmcmr, r-lsei
- Link Dependencies:
- r
- Run Dependencies:
- r-ggplot2, r-reshape2, r-complexheatmap, r-genomeinfodb, r-variantannotation, r, r-getoptlong, r-keggrest, r-corrplot, r-gtrellis, r-dendextend, r-genomicranges, r-gridextra, r-somaticsignatures, r-pmcmr, r-lsei
- Description:
- This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.
r-yaqcaffy¶
- Homepage:
- Spack package:
- Versions:
- 1.36.0
- Build Dependencies:
- r, r-simpleaffy
- Link Dependencies:
- r
- Run Dependencies:
- r, r-simpleaffy
- Description:
- Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
r-yarn¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- r, r-edger, r-limma, r-rcolorbrewer, r-quantro, r-gplots, r-biobase, r-biomart, r-matrixstats, r-preprocesscore, r-readr, r-downloader
- Link Dependencies:
- r
- Run Dependencies:
- r, r-edger, r-limma, r-rcolorbrewer, r-quantro, r-gplots, r-biobase, r-biomart, r-matrixstats, r-preprocesscore, r-readr, r-downloader
- Description:
- Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.
r-zlibbioc¶
- Homepage:
- Spack package:
- Versions:
- 1.22.0
- Build Dependencies:
- r
- Link Dependencies:
- r
- Run Dependencies:
- r
- Description:
- This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.
r-zoo¶
- Homepage:
- Spack package:
- Versions:
- 1.7-14, 1.7-13
- Build Dependencies:
- r, r-lattice
- Link Dependencies:
- r
- Run Dependencies:
- r, r-lattice
- Description:
- An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.
raft¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.2.3
- Build Dependencies:
- cuda, fftw, cmake, hdf5, mpi
- Link Dependencies:
- cuda, fftw, hdf5, mpi
- Description:
- RAFT: Reconstruct Algorithms for Tomography. Toolbox under development at Brazilian Synchrotron Light Source.
raja¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake
- Description:
- RAJA Parallel Framework.
randfold¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- squid
- Link Dependencies:
- squid
- Description:
- Minimum free energy of folding randomization test software
random123¶
- Homepage:
- Spack package:
- Versions:
- 1.09
- Description:
- Random123 is a library of 'counter-based' random number generators (CBRNGs), in which the Nth random number can be obtained by applying a stateless mixing function to N instead of the conventional approach of using N iterations of a stateful transformation.
randrproto¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Resize and Rotate Extension (RandR). This extension defines a protocol for clients to dynamically change X screens, so as to resize, rotate and reflect the root window of a screen.
ravel¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- otf2, qt, otf, muster, cmake
- Link Dependencies:
- otf2, qt, otf, muster
- Description:
- Ravel is a parallel communication trace visualization tool that orders events according to logical time.
raxml¶
- Homepage:
- Spack package:
- Versions:
- 8.2.11
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
ray¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- Parallel genome assemblies for parallel DNA sequencing
rdp-classifier¶
- Homepage:
- Spack package:
- Versions:
- 2.12
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
re2c¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Description:
- re2c: a free and open-source lexer generator for C and C++
readline¶
- Homepage:
- Spack package:
- Versions:
- 7.0, 6.3
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
recordproto¶
- Homepage:
- Spack package:
- Versions:
- 1.14.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Record Extension. This extension defines a protocol for the recording and playback of user actions in the X Window System.
redundans¶
- Homepage:
- Spack package:
- Versions:
- 0.13c
- Build Dependencies:
- py-pyscaf, snap-berkeley, gapcloser, bwa, perl, parallel, py-fastaindex, python, last, sspace-standard
- Link Dependencies:
- snap-berkeley, gapcloser, bwa, parallel, last, sspace-standard
- Run Dependencies:
- py-pyscaf, python, py-fastaindex, perl
- Description:
- Redundans pipeline assists an assembly of heterozygous genomes.
relion¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1, 2.0.3
- Build Dependencies:
- cuda, cmake, fftw, fltk, mpi
- Link Dependencies:
- cuda, fftw, fltk, mpi
- Description:
- RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
rempi¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- automake, autoconf, zlib, libtool, mpi
- Link Dependencies:
- zlib, mpi
- Description:
- ReMPI is a record-and-replay tool for MPI applications.
rename¶
- Homepage:
- Spack package:
- Versions:
- 1.600
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- Perl-powered file rename script with many helpful built-ins.
rendercheck¶
- Homepage:
- Spack package:
- Versions:
- 1.5
- Build Dependencies:
- pkgconfig, xproto, libxrender, libx11, util-macros
- Link Dependencies:
- libxrender, libx11
- Description:
- rendercheck is a program to test a Render extension implementation against separate calculations of expected output.
renderproto¶
- Homepage:
- Spack package:
- Versions:
- 0.11.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Rendering Extension. This extension defines the protcol for a digital image composition as the foundation of a new rendering model within the X Window System.
repeatmasker¶
- Homepage:
- Spack package:
- Versions:
- 4.0.7
- Build Dependencies:
- perl, hmmer, trf, ncbi-rmblastn
- Link Dependencies:
- hmmer, trf, ncbi-rmblastn
- Run Dependencies:
- perl
- Description:
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
resourceproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Resource Extension. This extension defines a protocol that allows a client to query the X server about its usage of various resources.
revbayes¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- cmake, boost, mpi
- Link Dependencies:
- boost, mpi
- Description:
- Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language.
rgb¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- xorg-server, xproto
- Link Dependencies:
- xorg-server
- Description:
- X color name database. This package includes both the list mapping X color names to RGB values (rgb.txt) and, if configured to use a database for color lookup, the rgb program to convert the text file into the binary database format. The "others" subdirectory contains some alternate color databases.
rhash¶
- Homepage:
- Spack package:
- Versions:
- 1.3.5
- Description:
- RHash is a console utility for computing and verifying hash sums of files. It supports CRC32, MD4, MD5, SHA1, SHA256, SHA512, SHA3, Tiger, TTH, Torrent BTIH, AICH, ED2K, GOST R 34.11-94, RIPEMD-160, HAS-160, EDON-R 256/512, WHIRLPOOL and SNEFRU hash sums.
rlwrap¶
- Homepage:
- Spack package:
- Versions:
- 0.43
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- rlwrap is a 'readline wrapper', a small utility that uses the GNU readline library to allow the editing of keyboard input for any command.
rmlab¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- pngwriter, cmake
- Link Dependencies:
- pngwriter
- Description:
- C++ File API for the reMarkable tablet
rna-seqc¶
- Homepage:
- Spack package:
- Versions:
- 1.1.8, 1.1.7, 1.1.6, 1.1.5, 1.1.4
- Run Dependencies:
- jdk
- Description:
- RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.
rockstar¶
- Homepage:
- Spack package:
- Versions:
- develop, yt
- Build Dependencies:
- hdf5
- Link Dependencies:
- hdf5
- Description:
- The Rockstar Halo Finder
root¶
- Homepage:
- Spack package:
- Versions:
- 6.09.02, 6.08.06, 6.06.08, 6.06.06, 6.06.04, 6.06.02, 5.34.36
- Build Dependencies:
- libpng, zlib, libsm, libxpm, pcre, jpeg, xz, libxext, fftw, freetype, libxft, cfitsio, libxml2, pkgconfig, python, binutils, cmake, libx11, sqlite, graphviz, openssl, gsl, libice
- Link Dependencies:
- libpng, zlib, sqlite, libxpm, python, binutils, pcre, jpeg, xz, libxext, fftw, freetype, libxft, libsm, graphviz, openssl, cfitsio, libxml2, gsl, libice, libx11
- Description:
- ROOT is a data analysis framework.
rose¶
- Homepage:
- Spack package:
- Versions:
- 0.9.7, master
- Build Dependencies:
- libgcrypt, z3, libtool, automake, java, autoconf, boost
- Link Dependencies:
- z3, java, boost
- Run Dependencies:
- py-binwalk
- Description:
- A compiler infrastructure to build source-to-source program transformation and analysis tools. (Developed at Lawrence Livermore National Lab)
rr¶
- Homepage:
- Spack package:
- Versions:
- 4.5.0, 4.4.0, 4.3.0
- Build Dependencies:
- gdb, zlib, pkgconfig, py-pexpect, cmake, git
- Link Dependencies:
- gdb, zlib, git
- Description:
- Application execution recorder, player and debugger
rsbench¶
- Homepage:
- Spack package:
- Versions:
- 2, 0
- Description:
- A mini-app to represent the multipole resonance representation lookup cross section algorithm.
rsem¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Build Dependencies:
- perl, r, star, bowtie2, bowtie, python
- Link Dependencies:
- star, bowtie2, bowtie
- Run Dependencies:
- perl, python, r
- Description:
- RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rstart¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, xproto, util-macros
- Description:
- This package includes both the client and server sides implementing the protocol described in the "A Flexible Remote Execution Protocol Based on rsh" paper found in the specs/ subdirectory. This software has been deprecated in favor of the X11 forwarding provided in common ssh implementations.
rsync¶
- Homepage:
- Spack package:
- Versions:
- 3.1.2, 3.1.1
- Description:
- An open source utility that provides fast incremental file transfer.
rtags¶
- Homepage:
- Spack package:
- Versions:
- 2.17
- Build Dependencies:
- llvm, zlib, pkgconfig, openssl, lua, cmake, bash-completion
- Link Dependencies:
- zlib, lua, llvm, openssl, bash-completion
- Description:
- RTags is a client/server application that indexes C/C++ code
rtax¶
- Homepage:
- Spack package:
- Versions:
- 0.984
- Build Dependencies:
- usearch
- Link Dependencies:
- usearch
- Description:
- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
ruby¶
- Homepage:
- Spack package:
- Versions:
- 2.2.0
- Build Dependencies:
- libffi, zlib, libx11, tcl, tk, openssl, readline
- Link Dependencies:
- libffi, zlib, libx11, tcl, tk, openssl, readline
- Description:
- A dynamic, open source programming language with a focus on simplicity and productivity.
ruby-gnuplot¶
- Homepage:
- Spack package:
- Versions:
- 2.6.2
- Build Dependencies:
- gnuplot, ruby
- Link Dependencies:
- gnuplot, ruby
- Description:
- Utility library to aid in interacting with gnuplot from ruby
ruby-narray¶
- Homepage:
- Spack package:
- Versions:
- 0.9.0.9
- Build Dependencies:
- ruby
- Link Dependencies:
- ruby
- Description:
- Numo::NArray is an Numerical N-dimensional Array class for fast processing and easy manipulation of multi-dimensional numerical data, similar to numpy.ndaray.
ruby-rubyinline¶
- Homepage:
- Spack package:
- Versions:
- 3.12.4
- Build Dependencies:
- ruby
- Link Dependencies:
- ruby
- Description:
- Inline allows you to write foreign code within your ruby code.
ruby-terminal-table¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- ruby
- Link Dependencies:
- ruby
- Description:
- Simple, feature rich ascii table generation library
rust¶
- Homepage:
- Spack package:
- Versions:
- 1.8.0
- Build Dependencies:
- llvm, openssl, cmake, curl, python, git
- Link Dependencies:
- llvm, openssl, cmake, curl, python, git
- Description:
- The rust programming language toolchain
rust-bindgen¶
- Homepage:
- Spack package:
- Versions:
- 0.20.5
- Build Dependencies:
- rust, llvm
- Link Dependencies:
- rust, llvm
- Description:
- The rust programming language toolchain
sabre¶
- Homepage:
- Spack package:
- Versions:
- 2013-09-27
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.
sailfish¶
- Homepage:
- Spack package:
- Versions:
- 0.10.1
- Build Dependencies:
- cmake, tbb, boost
- Link Dependencies:
- tbb, boost
- Description:
- Sailfish is a tool for transcript quantification from RNA-seq data.
salmon¶
- Homepage:
- Spack package:
- Versions:
- 0.9.1, 0.8.2
- Build Dependencies:
- cmake, tbb, boost
- Link Dependencies:
- tbb, boost
- Description:
- Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
sambamba¶
- Homepage:
- Spack package:
- Versions:
- 0.6.6
- Build Dependencies:
- python, ldc
- Link Dependencies:
- ldc
- Description:
- Sambamba: process your BAM data faster (bioinformatics)
samblaster¶
- Homepage:
- Spack package:
- Versions:
- 0.1.24, 0.1.23
- Description:
- A tool to mark duplicates and extract discordant and split reads from sam files.
samrai¶
- Homepage:
- Spack package:
- Versions:
- 3.11.2, 3.10.0, 3.9.1, 3.8.0, 3.7.3, 3.7.2, 3.6.3-beta, 3.5.2-beta, 3.5.0-beta, 3.4.1-beta, 3.3.3-beta, 3.3.2-beta, 2.4.4
- Build Dependencies:
- m4, zlib, boost, hdf5, mpi
- Link Dependencies:
- hdf5, zlib, boost, mpi
- Description:
- SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) is an object-oriented C++ software library enables exploration of numerical, algorithmic, parallel computing, and software issues associated with applying structured adaptive mesh refinement (SAMR) technology in large-scale parallel application development.
samtools¶
- Homepage:
- Spack package:
- Versions:
- 1.6, 1.4, 1.3.1, 1.2
- Build Dependencies:
- ncurses, htslib
- Link Dependencies:
- ncurses, htslib
- Description:
- SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
sandbox¶
- Homepage:
- Spack package:
- Versions:
- 2.12
- Description:
- sandbox'd LD_PRELOAD hack by Gentoo Linux
sas¶
- Homepage:
- Spack package:
- Versions:
- 0.2.0, 0.1.4, 0.1.3
- Build Dependencies:
- cmake, llvm, python
- Link Dependencies:
- llvm, python
- Description:
- SAS (Static Analysis Suite) is a powerful tool for running static analysis on C++ code.
satsuma2¶
- Homepage:
- Spack package:
- Versions:
- 2016-11-22
- Build Dependencies:
- cmake
- Description:
- Satsuma2 is an optimsed version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).
savanna¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.5
- Build Dependencies:
- tau, stc, adios, mpi, mpix-launch-swift
- Link Dependencies:
- tau, stc, adios, mpi, mpix-launch-swift
- Description:
- CODARcode Savanna runtime framework for high performance, workflow management using Swift/T and ADIOS.
saws¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.1.0
- Description:
- The Scientific Application Web server (SAWs) turns any C or C++ scientific or engineering application code into a webserver, allowing one to examine (and even modify) the state of the simulation with any browser from anywhere.
sbt¶
- Homepage:
- Spack package:
- Versions:
- 0.13.12
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Scala Build Tool
scala¶
- Homepage:
- Spack package:
- Versions:
- 2.20.6, 2.12.1, 2.11.11
- Build Dependencies:
- java
- Link Dependencies:
- java
- Description:
- Scala is a general-purpose programming language providing support for functional programming and a strong static type system. Designed to be concise, many of Scala's design decisions were designed to build from criticisms of Java.
scalasca¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1, 2.2.2, 2.1
- Build Dependencies:
- otf2, cube, mpi
- Link Dependencies:
- otf2, cube, mpi
- Description:
- Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those concerning communication and synchronization - and offers guidance in exploring their causes.
scalpel¶
- Homepage:
- Spack package:
- Versions:
- 0.5.3
- Build Dependencies:
- perl, cmake
- Link Dependencies:
- perl, cmake
- Description:
- Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology.
scan-for-matches¶
- Homepage:
- Spack package:
- Versions:
- 2010-7-16
- Description:
- scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.
scons¶
- Homepage:
- Spack package:
- Versions:
- 2.5.1, 2.5.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Run Dependencies:
- python
- Description:
- SCons is a software construction tool
scorec-core¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, zoltan, mpi
- Link Dependencies:
- zoltan, mpi
- Description:
- The SCOREC Core is a set of C/C++ libraries for unstructured mesh simulations on supercomputers.
scorep¶
- Homepage:
- Spack package:
- Versions:
- 3.1, 3.0, 2.0.2, 1.4.2, 1.3
- Build Dependencies:
- opari2, pdt, mpi, otf2, papi, cube
- Link Dependencies:
- opari2, pdt, mpi, otf2, papi, cube
- Description:
- The Score-P measurement infrastructure is a highly scalable and easy-to- use tool suite for profiling, event tracing, and online analysis of HPC applications.
scotch¶
- Homepage:
- Spack package:
- Versions:
- 6.0.4, 6.0.3, 6.0.0, 5.1.10b
- Build Dependencies:
- bison, flex, zlib, mpi
- Link Dependencies:
- zlib, mpi
- Description:
- Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering.
scr¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0, master
- Build Dependencies:
- dtcmp, zlib, libyogrt, mpi, pdsh, cmake
- Link Dependencies:
- dtcmp, zlib, libyogrt, mpi
- Run Dependencies:
- pdsh
- Description:
- SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes
screen¶
- Homepage:
- Spack package:
- Versions:
- 4.3.1, 4.3.0, 4.2.1, 4.2.0, 4.0.3, 4.0.2, 3.9.15, 3.9.11, 3.9.10, 3.9.9, 3.9.8, 3.9.4, 3.7.6, 3.7.4, 3.7.2, 3.7.1
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells.
scripts¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- Various X related scripts.
scrnsaverproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- MIT Screen Saver Extension. This extension defines a protocol to control screensaver features and also to query screensaver info on specific windows.
sctk¶
- Homepage:
- Spack package:
- Versions:
- 2.4.10, 2.4.9, 2.4.8, 2.4.0
- Description:
- The NIST Scoring Toolkit (SCTK) is a collection of software tools designed to score benchmark test evaluations of Automatic Speech Recognition (ASR) Systems. The toolkit is currently used by NIST, benchmark test participants, and reserchers worldwide to as a common scoring engine.
sdl2¶
- Homepage:
- Spack package:
- Versions:
- 2.0.5
- Build Dependencies:
- cmake
- Description:
- Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D.
sdl2-image¶
- Homepage:
- Spack package:
- Versions:
- 2.0.1
- Build Dependencies:
- sdl2
- Link Dependencies:
- sdl2
- Description:
- SDL is designed to provide the bare bones of creating a graphical program.
sed¶
- Homepage:
- Spack package:
- Versions:
- 4.2.2
- Description:
- GNU implementation of the famous stream editor.
seqprep¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Description:
- SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read.
seqtk¶
- Homepage:
- Spack package:
- Versions:
- 1.2, 1.1
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Toolkit for processing sequences in FASTA/Q formats.
serf¶
- Homepage:
- Spack package:
- Versions:
- 1.3.9, 1.3.8
- Build Dependencies:
- apr-util, openssl, zlib, apr, scons
- Link Dependencies:
- apr-util, openssl, zlib, apr
- Description:
- Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
sessreg¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- pkgconfig, xproto, util-macros
- Description:
- Sessreg is a simple program for managing utmp/wtmp entries for X sessions. It was originally written for use with xdm, but may also be used with other display managers such as gdm or kdm.
setxkbmap¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- pkgconfig, libxkbfile, libx11, util-macros
- Link Dependencies:
- libxkbfile, libx11
- Description:
- setxkbmap is an X11 client to change the keymaps in the X server for a specified keyboard to use the layout determined by the options listed on the command line.
sga¶
- Homepage:
- Spack package:
- Versions:
- 0.10.15, 0.10.14, 0.10.13, 0.10.12, 0.10.11, 0.10.10, 0.10.9, 0.10.8, 0.10.3
- Build Dependencies:
- autoconf, zlib, libtool, automake, bamtools, jemalloc, sparsehash
- Link Dependencies:
- sparsehash, zlib, bamtools, jemalloc
- Description:
- SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
shapeit¶
- Homepage:
- Spack package:
- Versions:
- 2.837
- Description:
- SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shiny-server¶
- Homepage:
- Spack package:
- Versions:
- 1.5.3.838
- Build Dependencies:
- python, git, openssl, cmake, r
- Link Dependencies:
- python, git, openssl, cmake, r
- Description:
- Shiny server lets you put shiny web applications and interactive documents online. Take your shiny apps and share them with your organization or the world.
shortstack¶
- Homepage:
- Spack package:
- Versions:
- 3.8.3
- Build Dependencies:
- perl, viennarna, samtools, bowtie
- Link Dependencies:
- viennarna, samtools, bowtie
- Run Dependencies:
- perl
- Description:
- ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.
showfont¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, libfs, util-macros
- Link Dependencies:
- libfs
- Description:
- showfont displays data about a font from an X font server. The information shown includes font information, font properties, character metrics, and character bitmaps.
sickle¶
- Homepage:
- Spack package:
- Versions:
- 1.33
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.
siesta¶
- Homepage:
- Spack package:
- Versions:
- 4.0.1, 3.2-pl-5
- Build Dependencies:
- netcdf, netcdf-fortran, mpi, lapack, scalapack, blas
- Link Dependencies:
- netcdf, netcdf-fortran, mpi, lapack, scalapack, blas
- Description:
- SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
signalp¶
- Homepage:
- Spack package:
- Versions:
- 4.1f
- Build Dependencies:
- gnuplot, perl
- Link Dependencies:
- gnuplot
- Run Dependencies:
- perl
- Description:
- SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. Note: A manual download is required for SignalP. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
signify¶
- Homepage:
- Spack package:
- Versions:
- 23
- Build Dependencies:
- libbsd
- Link Dependencies:
- libbsd
- Description:
- OpenBSD tool to signs and verify signatures on files.
silo¶
- Homepage:
- Spack package:
- Versions:
- 4.10.2, 4.9, 4.8
- Build Dependencies:
- qt, hdf5
- Link Dependencies:
- qt, hdf5
- Description:
- Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.
simplemoc¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- The purpose of this mini-app is to demonstrate the performance characterterics and viability of the Method of Characteristics (MOC) for 3D neutron transport calculations in the context of full scale light water reactor simulation.
simul¶
- Homepage:
- Spack package:
- Versions:
- 1.16, 1.15, 1.14, 1.13
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- simul is an MPI coordinated test of parallel filesystem system calls and library functions.
simulationio¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0.0, 0.1.0
- Build Dependencies:
- py-numpy, py-h5py, hdf5, cmake, swig, julia, python
- Link Dependencies:
- hdf5, python
- Run Dependencies:
- py-numpy, py-h5py, julia, python
- Description:
- SimulationIO: Efficient and convenient I/O for large PDE simulations
singularity¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.4, 2.3.1
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- Singularity is a container platform focused on supporting 'Mobility of Compute'
slepc¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.8.2, 3.8.0, 3.7.4, 3.7.3, 3.7.1, 3.6.3, 3.6.2
- Build Dependencies:
- python, petsc, arpack-ng
- Link Dependencies:
- arpack-ng, petsc
- Description:
- Scalable Library for Eigenvalue Problem Computations.
slurm¶
- Homepage:
- Spack package:
- Versions:
- 17-02-6-1
- Build Dependencies:
- munge, hdf5, zlib, pkgconfig, mariadb, curl, hwloc, gtkplus, lz4, glib, json-c, openssl, readline
- Link Dependencies:
- munge, hdf5, zlib, mariadb, curl, hwloc, gtkplus, lz4, glib, json-c, openssl, readline
- Description:
- Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Slurm requires no kernel modifications for its operation and is relatively self-contained. As a cluster workload manager, Slurm has three key functions. First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work.
smalt¶
- Homepage:
- Spack package:
- Versions:
- 0.7.6
- Description:
- SMALT aligns DNA sequencing reads with a reference genome.
smc¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- gmake, mpi
- Link Dependencies:
- mpi
- Description:
- A minimalist high-order finite difference algorithm for combustion problems. It includes core discretizations for advection, diffusive transport and chemical kinetics. The models for computing diffusive transport coefficients have been replaced by a simplified approximation but the full structure of the discretization of the diffusive terms have been preserved.
smproxy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- util-macros, libsm, libxt, pkgconfig, libxmu, libice
- Link Dependencies:
- libxmu, libice, libsm, libxt
- Description:
- smproxy allows X applications that do not support X11R6 session management to participate in an X11R6 session.
snakemake¶
- Homepage:
- Spack package:
- Versions:
- 3.11.2
- Build Dependencies:
- py-wrapt, python, py-setuptools, py-requests
- Link Dependencies:
- python
- Run Dependencies:
- py-wrapt, python, py-setuptools, py-requests
- Description:
- Snakemake is an MIT-licensed workflow management system.
snap¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- SNAP serves as a proxy application to model the performance of a modern discrete ordinates neutral particle transport application. SNAP may be considered an update to Sweep3D, intended for hybrid computing architectures. It is modeled off the Los Alamos National Laboratory code PARTISN.
snap-berkeley¶
- Homepage:
- Spack package:
- Versions:
- 1.0beta.18, 0.15
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.
snap-korf¶
- Homepage:
- Spack package:
- Versions:
- 2013-11-29
- Build Dependencies:
- perl, sparsehash, boost, sqlite
- Link Dependencies:
- sparsehash, boost, sqlite
- Run Dependencies:
- perl
- Description:
- SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
snappy¶
- Homepage:
- Spack package:
- Versions:
- 1.1.7
- Build Dependencies:
- cmake
- Description:
- A fast compressor/decompressor: https://code.google.com/p/snappy
snbone¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- metis
- Link Dependencies:
- metis
- Description:
- This application targets the primary computational solve burden of a SN, continuous finite element based transport equation solver.
sniffles¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7, 1.0.5
- Build Dependencies:
- cmake
- Description:
- Structural variation caller using third generation sequencing.
snptest¶
- Homepage:
- Spack package:
- Versions:
- 2.5.2
- Description:
- SNPTEST is a program for the analysis of single SNP association in genome-wide studies.
soap2¶
- Homepage:
- Spack package:
- Versions:
- 2.21
- Description:
- Software for short oligonucleotide alignment.
soapindel¶
- Homepage:
- Spack package:
- Versions:
- 2.1.7.17
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- SOAPindel is focusing on calling indels from the next-generation paired- end sequencing data.
soapsnp¶
- Homepage:
- Spack package:
- Versions:
- 1.03
- Build Dependencies:
- boost
- Link Dependencies:
- boost
- Description:
- SOAPsnp uses a method based on Bayes' theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors.
somatic-sniper¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5.0
- Build Dependencies:
- ncurses, cmake
- Link Dependencies:
- ncurses
- Description:
- A tool to call somatic single nucleotide variants.
sortmerna¶
- Homepage:
- Spack package:
- Versions:
- 2017-07-13
- Build Dependencies:
- cmake, zlib
- Link Dependencies:
- zlib
- Description:
- SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data
sosflow¶
- Homepage:
- Spack package:
- Versions:
- spack
- Build Dependencies:
- libevpath, cmake, sqlite
- Link Dependencies:
- libevpath, sqlite
- Description:
- SOSflow provides a flexible, scalable, and programmable framework for observation, introspection, feedback, and control of HPC applications.
sowing¶
- Homepage:
- Spack package:
- Versions:
- 1.1.23-p1
- Description:
- Sowing generates Fortran interfaces and documentation for PETSc and MPICH.
sox¶
- Homepage:
- Spack package:
- Versions:
- 14.4.2
- Build Dependencies:
- libvorbis, bzip2, id3lib, flac, opus
- Link Dependencies:
- libvorbis, bzip2, id3lib, flac, opus
- Description:
- SoX, the Swiss Army knife of sound processing programs.
spades¶
- Homepage:
- Spack package:
- Versions:
- 3.11.1, 3.10.1
- Build Dependencies:
- cmake, python, zlib, bzip2
- Link Dependencies:
- zlib, bzip2
- Run Dependencies:
- python
- Description:
- SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spark¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 2.0.2, 2.0.0, 1.6.2, 1.6.1, 1.6.0
- Build Dependencies:
- java, hadoop
- Run Dependencies:
- java, hadoop
- Description:
- Apache Spark is a fast and general engine for large-scale data processing.
sparsehash¶
- Homepage:
- Spack package:
- Versions:
- 2.0.3
- Description:
- Sparse and dense hash-tables for C++ by Google
sparta¶
- Homepage:
- Spack package:
- Versions:
- 1.25
- Build Dependencies:
- py-numpy, bowtie2, python, py-scipy
- Link Dependencies:
- bowtie2
- Run Dependencies:
- py-numpy, python, py-scipy
- Description:
- small RNA-PARE Target Analyzer (sPARTA) is a tool which utilizes high- throughput sequencing to profile genome-wide cleavage products.
spdlog¶
- Homepage:
- Spack package:
- Versions:
- 0.11.0, 0.10.0, 0.9.0
- Build Dependencies:
- cmake
- Description:
- Very fast, header only, C++ logging library
speex¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Description:
- Speex is an Open Source/Free Software patent-free audio compression format designed for speech.
sph2pipe¶
- Homepage:
- Spack package:
- Versions:
- 2.5
- Build Dependencies:
- cmake
- Description:
- Sph2pipe is a portable tool for converting SPHERE files to other formats.
spherepack¶
- Homepage:
- Spack package:
- Versions:
- 3.2
- Description:
- SPHEREPACK - A Package for Modeling Geophysical Processes
spindle¶
- Homepage:
- Spack package:
- Versions:
- 0.8.1
- Build Dependencies:
- launchmon
- Link Dependencies:
- launchmon
- Description:
- Spindle improves the library-loading performance of dynamically linked HPC applications. Without Spindle large MPI jobs can overload on a shared file system when loading dynamically linked libraries, causing site-wide performance problems.
spot¶
- Homepage:
- Spack package:
- Versions:
- 1.99.3, 1.2.6
- Build Dependencies:
- python, boost
- Link Dependencies:
- python, boost
- Description:
- Spot is a C++11 library for omega-automata manipulation and model checking.
sqlite¶
- Homepage:
- Spack package:
- Versions:
- 3.21.0, 3.20.0, 3.18.0, 3.8.10.2, 3.8.5
- Build Dependencies:
- readline
- Link Dependencies:
- readline
- Description:
- SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without running a separate RDBMS process.
squid¶
- Homepage:
- Spack package:
- Versions:
- 1.9g
- Description:
- C function library for sequence analysis.
sra-toolkit¶
- Homepage:
- Spack package:
- Versions:
- 2.8.2-1
- Description:
- The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
sspace-longread¶
- Homepage:
- Spack package:
- Versions:
- 1.1
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads Note: A manual download is required for SSPACE- LongRead. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
sspace-standard¶
- Homepage:
- Spack package:
- Versions:
- 3.0
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data Note: A manual download is required for SSPACE-Standard. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
sst-dumpi¶
- Homepage:
- Spack package:
- Versions:
- 6.1.0, master
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- The DUMPI package provides libraries to collect and read traces of MPI applications. Traces are created by linking an application with a library that uses the PMPI interface to intercept MPI calls. DUMPI records signatures of all MPI-1 and MPI-2 subroutine calls, return values, request information, and PAPI counters.
sst-macro¶
- Homepage:
- Spack package:
- Versions:
- 6.1.0, master
- Build Dependencies:
- automake, autoconf, m4, boost, libtool
- Link Dependencies:
- boost
- Description:
- The SST/macro software package provides a simulator for large-scale parallel computer architectures for the coarse-grained study of distributed-memory applications. The simulator is driven from either a trace file or skeleton application. SST/macro's modular architecture can be extended with additional network models, trace file formats, software services, and processor models.
stacks¶
- Homepage:
- Spack package:
- Versions:
- 1.46
- Build Dependencies:
- perl, sparsehash
- Link Dependencies:
- sparsehash
- Run Dependencies:
- perl
- Description:
- Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.
staden-io-lib¶
- Homepage:
- Spack package:
- Versions:
- 1.14.8
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Io_lib is a library for reading/writing various bioinformatics file formats.
star¶
- Homepage:
- Spack package:
- Versions:
- 2.5.3a, 2.4.2a
- Description:
- STAR is an ultrafast universal RNA-seq aligner.
star-ccm-plus¶
- Homepage:
- Spack package:
- Versions:
- 11.06.010_02
- Description:
- STAR-CCM+ (Computational Continuum Mechanics) CFD solver.
startup-notification¶
- Homepage:
- Spack package:
- Versions:
- 0.12
- Build Dependencies:
- libxcb, libx11, xcb-util
- Link Dependencies:
- libxcb, libx11, xcb-util
- Description:
- startup-notification contains a reference implementation of the freedesktop startup notification protocol.
stat¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1, 3.0.0, 2.2.0, 2.1.0, 2.0.0
- Build Dependencies:
- graphlib, libtool, py-pygtk, automake, dyninst, mpi, mrnet, autoconf, libdwarf, graphviz, swig, launchmon, python
- Link Dependencies:
- graphlib, libdwarf, mpi, swig, dyninst, graphviz, python, launchmon, mrnet
- Run Dependencies:
- graphviz, py-pygtk
- Description:
- Library to create, manipulate, and export graphs Graphlib.
stc¶
- Homepage:
- Spack package:
- Versions:
- 0.7.3
- Build Dependencies:
- turbine, java, ant
- Link Dependencies:
- turbine, java, ant
- Run Dependencies:
- zsh
- Description:
- STC: The Swift-Turbine Compiler
stream¶
- Homepage:
- Spack package:
- Versions:
- 5.10
- Description:
- The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.
strelka¶
- Homepage:
- Spack package:
- Versions:
- 2.8.2
- Build Dependencies:
- cmake, python, boost, zlib, bzip2
- Link Dependencies:
- cmake, python, boost, zlib, bzip2
- Description:
- Somatic and germline small variant caller for mapped sequencing data.
stress¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Description:
- stress is a deliberately simple workload generator for POSIX systems. It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system. It is written in C, and is free software licensed under the GPLv2.
stringtie¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4a, 1.3.3b
- Build Dependencies:
- samtools
- Link Dependencies:
- samtools
- Description:
- StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
structure¶
- Homepage:
- Spack package:
- Versions:
- 2.3.4
- Build Dependencies:
- jdk
- Run Dependencies:
- jdk
- Description:
- Structure is a free software package for using multi-locus genotype data to investigate population structure.
sublime-text¶
- Homepage:
- Spack package:
- Versions:
- 3_build_3126, 2.0.2
- Run Dependencies:
- libffi, libx11, libxau, pcre, libxcb, glib
- Description:
- Sublime Text is a sophisticated text editor for code, markup and prose.
subread¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0, 1.5.2
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- The Subread software package is a tool kit for processing next-gen sequencing data.
subversion¶
- Homepage:
- Spack package:
- Versions:
- 1.9.5, 1.9.3, 1.8.17, 1.8.13
- Build Dependencies:
- perl, zlib, apr, sqlite, serf, apr-util, swig, perl-term-readkey
- Link Dependencies:
- perl, zlib, apr, sqlite, serf, apr-util, swig, perl-term-readkey
- Description:
- Apache Subversion - an open source version control system.
suite-sparse¶
- Homepage:
- Spack package:
- Versions:
- 5.1.0, 4.5.5, 4.5.4, 4.5.3, 4.5.1
- Build Dependencies:
- lapack, cuda, metis, tbb, blas
- Link Dependencies:
- lapack, cuda, metis, tbb, blas
- Description:
- SuiteSparse is a suite of sparse matrix algorithms
sumaclust¶
- Homepage:
- Spack package:
- Versions:
- 1.0.20
- Description:
- Sumaclust aims to cluster sequences in a way that is fast and exact at the same time.
sundials¶
- Homepage:
- Spack package:
- Versions:
- 3.1.0, 3.0.0, 2.7.0, 2.6.2
- Build Dependencies:
- cuda, hypre, petsc, cmake, mpi, lapack, raja, suite-sparse, superlu-mt, blas
- Link Dependencies:
- cuda, hypre, petsc, mpi, lapack, raja, suite-sparse, superlu-mt, blas
- Description:
- SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)
superlu¶
- Homepage:
- Spack package:
- Versions:
- 5.2.1, 4.3
- Build Dependencies:
- cmake, blas
- Link Dependencies:
- blas
- Description:
- SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU is designed for sequential machines.
superlu-dist¶
- Homepage:
- Spack package:
- Versions:
- develop, 5.2.2, 5.2.1, 5.1.3, 5.1.1, 5.1.0, 5.0.0, 4.3, 4.2, 4.1, 4.0, 3.3, xsdk-0.2.0
- Build Dependencies:
- lapack, metis, blas, mpi, parmetis
- Link Dependencies:
- lapack, metis, blas, mpi, parmetis
- Description:
- A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
superlu-mt¶
- Homepage:
- Spack package:
- Versions:
- 3.1
- Build Dependencies:
- blas
- Link Dependencies:
- blas
- Description:
- SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU_MT is designed for shared memory parallel machines.
sw4lite¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- lapack, blas, mpi
- Link Dependencies:
- lapack, blas, mpi
- Description:
- Sw4lite is a bare bone version of SW4 intended for testing performance optimizations in a few important numerical kernels of SW4.
swarm¶
- Homepage:
- Spack package:
- Versions:
- 2.1.13
- Description:
- A robust and fast clustering method for amplicon-based studies.
swfft¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- fftw, mpi
- Link Dependencies:
- fftw, mpi
- Description:
- A stand-alone version of HACC's distributed-memory, pencil-decomposed, parallel 3D FFT.
swiftsim¶
- Homepage:
- Spack package:
- Versions:
- 0.3.0
- Build Dependencies:
- autoconf, m4, libtool, mpi, automake, metis, hdf5
- Link Dependencies:
- metis, hdf5, mpi
- Description:
- SPH With Inter-dependent Fine-grained Tasking (SWIFT) provides astrophysicists with a state of the art framework to perform particle based simulations.
swig¶
- Homepage:
- Spack package:
- Versions:
- 3.0.12, 3.0.11, 3.0.10, 3.0.8, 3.0.2, 2.0.12, 2.0.2, 1.3.40
- Build Dependencies:
- pcre
- Link Dependencies:
- pcre
- Description:
- SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application.
symengine¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.3.0, 0.2.0, 0.1.0
- Build Dependencies:
- flint, llvm, mpc, boost, mpfr, cmake, piranha, gmp
- Link Dependencies:
- flint, llvm, mpc, boost, mpfr, piranha, gmp
- Description:
- SymEngine is a fast symbolic manipulation library, written in C++.
sympol¶
- Homepage:
- Spack package:
- Versions:
- 0.1.8
- Build Dependencies:
- bliss, lrslib, cmake, boost, gmp
- Link Dependencies:
- bliss, lrslib, boost, gmp
- Description:
- SymPol is a C++ tool to work with symmetric polyhedra
sz¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.4.11.0, 1.4.10.0, 1.4.9.2
- Description:
- Error-bounded Lossy Compressor for HPC Data.
tabix¶
- Homepage:
- Spack package:
- Versions:
- 2013-12-16
- Build Dependencies:
- perl, python
- Run Dependencies:
- perl, python
- Description:
- Generic indexer for TAB-delimited genome position files
talloc¶
- Homepage:
- Spack package:
- Versions:
- 2.1.9
- Description:
- Talloc provides a hierarchical, reference counted memory pool system with destructors. It is the core memory allocator used in Samba.
tantan¶
- Homepage:
- Spack package:
- Versions:
- 13
- Description:
- tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.
tar¶
- Homepage:
- Spack package:
- Versions:
- 1.29, 1.28
- Description:
- GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.
targetp¶
- Homepage:
- Spack package:
- Versions:
- 1.1b
- Build Dependencies:
- chlorop, signalp
- Link Dependencies:
- chlorop, signalp
- Run Dependencies:
- awk, perl
- Description:
- TargetP predicts the subcellular location of eukaryotic protein sequences. Note: A manual download is required for TargetP. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
task¶
- Homepage:
- Spack package:
- Versions:
- 2.4.4
- Build Dependencies:
- libuuid, cmake, gnutls
- Link Dependencies:
- libuuid, gnutls
- Description:
- Feature-rich console based todo list manager
taskd¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- libuuid, cmake, gnutls
- Link Dependencies:
- libuuid, gnutls
- Description:
- TaskWarrior task synchronization daemon
tasmanian¶
- Homepage:
- Spack package:
- Versions:
- 5.0
- Build Dependencies:
- cmake
- Description:
- The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN is a robust library for high dimensional integration and interpolation as well as parameter calibration.
tassel¶
- Homepage:
- Spack package:
- Versions:
- 2017-07-22
- Build Dependencies:
- perl, java
- Run Dependencies:
- perl, java
- Description:
- TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tau¶
- Homepage:
- Spack package:
- Versions:
- 2.25, 2.24.1, 2.24, 2.23.1
- Build Dependencies:
- scorep, binutils, pdt, mpi
- Link Dependencies:
- scorep, binutils, pdt, mpi
- Description:
- A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.
tcl¶
- Homepage:
- Spack package:
- Versions:
- 8.6.6, 8.6.5, 8.6.4, 8.6.3, 8.5.19
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible.
tcoffee¶
- Homepage:
- Spack package:
- Versions:
- 2017-08-17
- Build Dependencies:
- perl, blast-plus, viennarna, mafft, clustalw, pcma, dialign-tx, probconsrna, poamsa, muscle, tmalign
- Link Dependencies:
- clustalw, viennarna, mafft, blast-plus, pcma, dialign-tx, probconsrna, poamsa, muscle, tmalign
- Run Dependencies:
- perl
- Description:
- T-Coffee is a multiple sequence alignment program.
tcsh¶
- Homepage:
- Spack package:
- Versions:
- 6.20.00
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- Tcsh is an enhanced but completely compatible version of csh, the C shell. Tcsh is a command language interpreter which can be used both as an interactive login shell and as a shell script command processor. Tcsh includes a command line editor, programmable word completion, spelling correction, a history mechanism, job control and a C language like syntax.
tealeaf¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- Proxy Application. TeaLeaf is a mini-app that solves the linear heat conduction equation on a spatially decomposed regularly grid using a 5 point stencil with implicit solvers.
tetgen¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0, 1.4.3
- Description:
- TetGen is a program and library that can be used to generate tetrahedral meshes for given 3D polyhedral domains. TetGen generates exact constrained Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and Voronoi paritions.
tethex¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.0.7
- Build Dependencies:
- cmake
- Description:
- Tethex is designed to convert triangular (in 2D) or tetrahedral (in 3D) Gmsh's mesh to quadrilateral or hexahedral one respectively. These meshes can be used in software packages working with hexahedrals only - for example, deal.II.
texinfo¶
- Homepage:
- Spack package:
- Versions:
- 6.5, 6.3, 6.0, 5.2, 5.1, 5.0
- Description:
- Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob Chassell many years ago, loosely based on Brian Reid's Scribe and other formatting languages of the time. It is used by many non-GNU projects as well.
texlive¶
- Homepage:
- Spack package:
- Versions:
- live
- Build Dependencies:
- perl
- Description:
- TeX Live is a free software distribution for the TeX typesetting system. Heads up, it's is not a reproducible installation.
the-platinum-searcher¶
- Homepage:
- Spack package:
- Versions:
- head
- Build Dependencies:
- go
- Link Dependencies:
- go
- Description:
- Fast parallel recursive grep alternative
the-silver-searcher¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 0.32.0, 0.30.0
- Build Dependencies:
- pkgconfig, pcre, zlib, xz
- Link Dependencies:
- pcre, zlib, xz
- Description:
- Fast recursive grep alternative
thrift¶
- Homepage:
- Spack package:
- Versions:
- 0.10.0, 0.9.3, 0.9.2
- Build Dependencies:
- autoconf, openssl, libtool, bison, flex, java, automake, python, zlib, libevent, boost
- Link Dependencies:
- openssl, zlib, libevent, python, java, boost
- Description:
- Software framework for scalable cross-language services development. Thrift combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages.
thrust¶
- Homepage:
- Spack package:
- Versions:
- 1.8.2
- Description:
- Thrust is a parallel algorithms library which resembles the C++ Standard Template Library (STL).
tig¶
- Homepage:
- Spack package:
- Versions:
- 2.2.2
- Build Dependencies:
- ncurses
- Link Dependencies:
- ncurses
- Description:
- Text-mode interface for git
tinyxml¶
- Homepage:
- Spack package:
- Versions:
- 2.6.2
- Build Dependencies:
- cmake
- Description:
- Simple, small, efficient, C++ XML parser
tinyxml2¶
- Homepage:
- Spack package:
- Versions:
- 4.0.1, 4.0.0, 3.0.0, 2.2.0, 2.1.0, 2.0.2
- Build Dependencies:
- cmake
- Description:
- Simple, small, efficient, C++ XML parser
tioga¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- Topology Independent Overset Grid Assembly (TIOGA)
tk¶
- Homepage:
- Spack package:
- Versions:
- 8.6.6, 8.6.5, 8.6.3
- Build Dependencies:
- tcl, libx11
- Link Dependencies:
- tcl, libx11
- Description:
- Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more.
tmalign¶
- Homepage:
- Spack package:
- Versions:
- 2016-05-25
- Description:
- TM-align is an algorithm for sequence-order independent protein structure comparisons.
tmhmm¶
- Homepage:
- Spack package:
- Versions:
- 2.0c
- Run Dependencies:
- perl
- Description:
- Transmembrane helices in proteins Note: A manual download is required for TMHMM. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
tmux¶
- Homepage:
- Spack package:
- Versions:
- 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 1.9a
- Build Dependencies:
- ncurses, libevent
- Link Dependencies:
- ncurses, libevent
- Description:
- Tmux is a terminal multiplexer. What is a terminal multiplexer? It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. And do a lot more.
tmuxinator¶
- Homepage:
- Spack package:
- Versions:
- 0.6.11
- Build Dependencies:
- ruby
- Link Dependencies:
- ruby
- Description:
- A session configuration creator and manager for tmux
tophat¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1
- Build Dependencies:
- automake, autoconf, m4, libtool, boost
- Link Dependencies:
- boost
- Run Dependencies:
- bowtie2
- Description:
- Spliced read mapper for RNA-Seq.
tppred¶
- Homepage:
- Spack package:
- Versions:
- 2.0
- Build Dependencies:
- emboss
- Link Dependencies:
- emboss
- Run Dependencies:
- py-scikit-learn, python
- Description:
- TPPRED is a software package for the prediction of mitochondrial targeting peptides from protein primary sequence.
transabyss¶
- Homepage:
- Spack package:
- Versions:
- 1.5.5
- Build Dependencies:
- blat, py-igraph, python, abyss
- Link Dependencies:
- blat, abyss
- Run Dependencies:
- py-igraph, python
- Description:
- De novo assembly of RNAseq data using ABySS
transdecoder¶
- Homepage:
- Spack package:
- Versions:
- 3.0.1
- Build Dependencies:
- perl
- Run Dependencies:
- perl
- Description:
- TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
transposome¶
- Homepage:
- Spack package:
- Versions:
- 0.11.2
- Build Dependencies:
- perl, blast-plus
- Link Dependencies:
- perl, blast-plus
- Run Dependencies:
- perl
- Description:
- A toolkit for annotation of transposable element families from unassembled sequence reads.
transset¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- transset is an utility for setting opacity property.
tree¶
- Homepage:
- Spack package:
- Versions:
- 1.7.0
- Description:
- Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty. Tree has been ported and reported to work under the following operating systems: Linux, FreeBSD, OS X, Solaris, HP/UX, Cygwin, HP Nonstop and OS/2.
trf¶
- Homepage:
- Spack package:
- Versions:
- 4.09
- Description:
- Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. Note: A manual download is required for TRF. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
triangle¶
- Homepage:
- Spack package:
- Versions:
- 1.6
- Description:
- Triangle is a two-dimensional mesh generator and Delaunay triangulator. Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes.
trilinos¶
- Homepage:
- Spack package:
- Versions:
- develop, 12.12.1, 12.10.1, 12.8.1, 12.6.4, 12.6.3, 12.6.2, 12.6.1, 12.4.2, 12.2.1, 12.0.1, 11.14.3, 11.14.2, 11.14.1, xsdk-0.2.0, master
- Build Dependencies:
- py-numpy, hdf5, zlib, lapack, suite-sparse, mumps, superlu-dist, swig, cgns, netcdf, hypre, metis, parmetis, superlu, scalapack, cmake, boost, matio, mpi, glm, python, blas
- Link Dependencies:
- netcdf, hypre, metis, hdf5, zlib, parmetis, lapack, scalapack, mpi, suite-sparse, superlu, boost, matio, mumps, superlu-dist, swig, cgns, blas, python, glm
- Run Dependencies:
- py-numpy
- Description:
- The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
trimgalore¶
- Homepage:
- Spack package:
- Versions:
- 0.4.5, 0.4.4
- Build Dependencies:
- perl, py-cutadapt, fastqc
- Link Dependencies:
- fastqc
- Run Dependencies:
- perl, py-cutadapt
- Description:
- Trim Galore! is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
trimmomatic¶
- Homepage:
- Spack package:
- Versions:
- 0.36, 0.33
- Run Dependencies:
- java
- Description:
- A flexible read trimming tool for Illumina NGS data.
turbine¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- adlbx, tcl, zsh, swig
- Link Dependencies:
- adlbx, tcl, zsh, swig
- Description:
- Turbine: The Swift/T runtime
turbomole¶
- Homepage:
- Spack package:
- Versions:
- 7.0.2
- Description:
- TURBOMOLE: Program Package for ab initio Electronic Structure Calculations. Note: Turbomole requires purchase of a license to download. Go to the Turbomole home page, http://www.turbomole-gmbh.com, for details. Spack will search the current directory for this file. It is probably best to add this file to a Spack mirror so that it can be found from anywhere. For information on setting up a Spack mirror see http://spack.readthedocs.io/en/latest/mirrors.html
tut¶
- Homepage:
- Spack package:
- Versions:
- 2016-12-19
- Build Dependencies:
- python
- Description:
- TUT is a small and portable unit test framework for C++.
twm¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- libxext, libx11, libsm, libxt, pkgconfig, libxmu, flex, bison, libice, util-macros, xproto
- Link Dependencies:
- libxext, libx11, libsm, libxt, libxmu, libice
- Description:
- twm is a window manager for the X Window System. It provides titlebars, shaped windows, several forms of icon management, user-defined macro functions, click-to-type and pointer-driven keyboard focus, and user- specified key and pointer button bindings.
tycho2¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- A neutral particle transport mini-app to study performance of sweeps on unstructured, 3D tetrahedral meshes.
typhonio¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.6_CMake
- Build Dependencies:
- hdf5, cmake, mpi
- Link Dependencies:
- hdf5, mpi
- Description:
- TyphonIO is a library of routines that perform input/output (I/O) of scientific data within application codes
uberftp¶
- Homepage:
- Spack package:
- Versions:
- 2_8, 2_7, 2_6
- Build Dependencies:
- globus-toolkit
- Link Dependencies:
- globus-toolkit
- Description:
- UberFTP is an interactive (text-based) client for GridFTP
ucx¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2, 1.2.1
- Description:
- a communication library implementing high-performance messaging for MPI/PGAS frameworks
udunits2¶
- Homepage:
- Spack package:
- Versions:
- 2.2.24, 2.2.23, 2.2.21
- Build Dependencies:
- expat
- Link Dependencies:
- expat
- Description:
- Automated units conversion
ufo-core¶
- Homepage:
- Spack package:
- Versions:
- 0.14.0
- Build Dependencies:
- cmake, json-glib, glib
- Link Dependencies:
- json-glib, glib
- Description:
- The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. This package contains the run-time system and development files.
ufo-filters¶
- Homepage:
- Spack package:
- Versions:
- 0.14.1
- Build Dependencies:
- ufo-core, cmake
- Link Dependencies:
- ufo-core
- Description:
- The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. This package contains filter plugins.
unblur¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- fftw, zlib, libtiff, gsl, jpeg, jbigkit
- Link Dependencies:
- fftw, zlib, libtiff, gsl, jpeg, jbigkit
- Description:
- Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion.
uncrustify¶
- Homepage:
- Spack package:
- Versions:
- 0.61
- Description:
- Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others.
unison¶
- Homepage:
- Spack package:
- Versions:
- 2.48.4
- Build Dependencies:
- ocaml
- Description:
- Unison is a file-synchronization tool for OSX, Unix, and Windows. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other.
units¶
- Homepage:
- Spack package:
- Versions:
- 2.13
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- GNU units converts between different systems of units
unixodbc¶
- Homepage:
- Spack package:
- Versions:
- 2.3.4
- Build Dependencies:
- libtool, libiconv
- Link Dependencies:
- libtool, libiconv
- Description:
- ODBC is an open specification for providing application developers with a predictable API with which to access Data Sources. Data Sources include SQL Servers and any Data Source with an ODBC Driver.
usearch¶
- Homepage:
- Spack package:
- Versions:
- 10.0.240
- Description:
- USEARCH is a unique sequence analysis tool with thousands of users world-wide. Note: A manual download is required for USEARCH. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
util-linux¶
- Homepage:
- Spack package:
- Versions:
- 2.29.2, 2.29.1, 2.25
- Build Dependencies:
- python
- Link Dependencies:
- python
- Description:
- Util-linux is a suite of essential utilities for any Linux system.
util-macros¶
- Homepage:
- Spack package:
- Versions:
- 1.19.1, 1.19.0
- Description:
- This is a set of autoconf macros used by the configure.ac scripts in other Xorg modular packages, and is needed to generate new versions of their configure scripts with autoconf.
uuid¶
- Homepage:
- Spack package:
- Versions:
- 1.6.2
- Description:
- OSSP uuid is a ISO-C:1999 application programming interface (API) and corresponding command line interface (CLI) for the generation of DCE 1.1, ISO/IEC 11578:1996 and RFC 4122 compliant Universally Unique Identifier (UUID).
valgrind¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.13.0, 3.12.0, 3.11.0, 3.10.1, 3.10.0
- Build Dependencies:
- automake, autoconf, mpi, libtool, boost
- Link Dependencies:
- boost, mpi
- Description:
- An instrumentation framework for building dynamic analysis. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2.
vampirtrace¶
- Homepage:
- Spack package:
- Versions:
- 5.14.4
- Build Dependencies:
- otf, papi, zlib, mpi
- Link Dependencies:
- otf, papi, zlib, mpi
- Description:
- VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP, Pthreads).
vardictjava¶
- Homepage:
- Spack package:
- Versions:
- 1.5.1
- Run Dependencies:
- java
- Description:
- VarDictJava is a variant discovery program written in Java. It is a partial Java port of VarDict variant caller.
varscan¶
- Homepage:
- Spack package:
- Versions:
- 2.4.2
- Build Dependencies:
- java
- Run Dependencies:
- java
- Description:
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vc¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0, 1.2.0, 1.1.0
- Build Dependencies:
- cmake
- Description:
- SIMD Vector Classes for C++
vcftools¶
- Homepage:
- Spack package:
- Versions:
- 0.1.14
- Build Dependencies:
- perl, zlib
- Link Dependencies:
- zlib
- Run Dependencies:
- perl
- Description:
- VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
vcsh¶
- Homepage:
- Spack package:
- Versions:
- 1.20151229-1, 1.20151229, 1.20150502, 1.20141026, 1.20141025
- Run Dependencies:
- git
- Description:
- config manager based on git
vdt¶
- Homepage:
- Spack package:
- Versions:
- 0.3.9, 0.3.8, 0.3.7, 0.3.6
- Build Dependencies:
- cmake
- Description:
- Vectorised math. A collection of fast and inline implementations of mathematical functions.
vecgeom¶
- Homepage:
- Spack package:
- Versions:
- 0.3.rc
- Build Dependencies:
- cmake
- Description:
- The vectorized geometry library for particle-detector simulation (toolkits).
veclibfort¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.4.2
- Description:
- Lightweight but flexible shim designed to rectify the incompatibilities between the Accelerate/vecLib BLAS and LAPACK libraries shipped with macOS and FORTRAN code compiled with modern compilers such as GNU Fortran.
vegas2¶
- Homepage:
- Spack package:
- Versions:
- 2
- Build Dependencies:
- plink
- Link Dependencies:
- plink
- Run Dependencies:
- perl, r-corpcor, r-mvtnorm, r
- Description:
- "VEGAS2 is an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X
velvet¶
- Homepage:
- Spack package:
- Versions:
- 1.2.10
- Description:
- Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.
videoproto¶
- Homepage:
- Spack package:
- Versions:
- 2.3.3
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Video Extension. This extension provides a protocol for a video output mechanism, mainly to rescale video playback in the video controller hardware.
viennarna¶
- Homepage:
- Spack package:
- Versions:
- 2.4.3, 2.3.5
- Build Dependencies:
- perl, python, libsvm, gsl
- Link Dependencies:
- gsl, libsvm
- Run Dependencies:
- perl, python
- Description:
- The ViennaRNA Package consists of a C code library and several stand- alone programs for the prediction and comparison of RNA secondary structures.
viewres¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, libxaw, libxmu, util-macros, libxt
- Link Dependencies:
- libxaw, libxmu, libxt
- Description:
- viewres displays a tree showing the widget class hierarchy of the Athena Widget Set (libXaw).
vim¶
- Homepage:
- Spack package:
- Versions:
- 8.0.1376, 8.0.0503, 8.0.0454, 8.0.0134, 7.4.2367
- Build Dependencies:
- perl, ncurses, python, lua, ruby
- Link Dependencies:
- perl, ncurses, python, lua, ruby
- Run Dependencies:
- cscope
- Description:
- Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often called a "programmer's editor," and so useful for programming that many consider it an entire IDE. It's not just for programmers, though. Vim is perfect for all kinds of text editing, from composing email to editing configuration files.
virtualgl¶
- Homepage:
- Spack package:
- Versions:
- 2.5.2
- Build Dependencies:
- cmake, mesa-glu, libjpeg-turbo
- Link Dependencies:
- mesa-glu, libjpeg-turbo
- Description:
- VirtualGL redirects 3D commands from a Unix/Linux OpenGL application onto a server-side GPU and converts the rendered 3D images into a video stream with which remote clients can interact to view and control the 3D application in real time.
visit¶
- Homepage:
- Spack package:
- Versions:
- 2.13.0, 2.12.3, 2.12.2, 2.10.3, 2.10.2, 2.10.1
- Build Dependencies:
- qwt, silo, hdf5, python, qt, cmake, vtk
- Link Dependencies:
- qwt, silo, hdf5, qt, python, vtk
- Description:
- VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
vizglow¶
- Homepage:
- Spack package:
- Versions:
- 2.2alpha20, 2.2alpha17, 2.2alpha15
- Build Dependencies:
- fontconfig, libxrender, xterm, libcanberra, freetype, zlib
- Link Dependencies:
- fontconfig, libxrender, xterm, libcanberra, freetype, zlib
- Description:
- VizGlow software tool is used for high-fidelity multi-dimensional modeling of non-equilibrium plasma discharges. Note: VizGlow is licensed software. You will need to create an account on the EsgeeTech homepage and download VizGlow yourself. Spack will search your current directory for a file of this format. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
vmatch¶
- Homepage:
- Spack package:
- Versions:
- 2.3.0
- Description:
- Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks
voropp¶
- Homepage:
- Spack package:
- Versions:
- 0.4.6
- Description:
- Voro++ is a open source software library for the computation of the Voronoi diagram, a widely-used tessellation that has applications in many scientific fields.
votca-csg¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.4.1, 1.4
- Build Dependencies:
- votca-tools, gromacs, cmake
- Link Dependencies:
- votca-tools, gromacs
- Description:
- Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA coarse-graining engine.
votca-ctp¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- votca-moo, votca-tools, cmake, votca-csg
- Link Dependencies:
- votca-moo, votca-tools, votca-csg
- Description:
- Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA charge transport engine.
votca-moo¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- votca-tools, cmake
- Link Dependencies:
- votca-tools
- Description:
- Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA molecular orbital module.
votca-tools¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.4.1, 1.4
- Build Dependencies:
- fftw, boost, sqlite, expat, cmake, gsl
- Link Dependencies:
- expat, fftw, gsl, boost, sqlite
- Description:
- Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the basic tools library of VOTCA.
votca-xtp¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.4.1
- Build Dependencies:
- votca-moo, votca-tools, votca-ctp, votca-csg, cmake
- Link Dependencies:
- votca-moo, votca-tools, votca-ctp, votca-csg
- Description:
- Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA exciton transport engine.
vpfft¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- eigen, fftw, mpi
- Link Dependencies:
- eigen, fftw, mpi
- Description:
- Proxy Application. VPFFT is an implementation of a mesoscale micromechanical materials model. By solving the viscoplasticity model, VPFFT simulates the evolution of a material under deformation. The solution time to the viscoplasticity model, described by a set of partial differential equations, is significantly reduced by the application of Fast Fourier Transform in the VPFFT algorithm.
vpic¶
- Homepage:
- Spack package:
- Versions:
- develop
- Build Dependencies:
- cmake, mpi
- Link Dependencies:
- mpi
- Description:
- VPIC is a general purpose particle-in-cell simulation code for modeling kinetic plasmas in one, two, or three spatial dimensions. It employs a second-order, explicit, leapfrog algorithm to update charged particle positions and velocities in order to solve the relativistic kinetic equation for each species in the plasma, along with a full Maxwell description for the electric and magnetic fields evolved via a second- order finite-difference-time-domain (FDTD) solve.
vsearch¶
- Homepage:
- Spack package:
- Versions:
- 2.4.3
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- VSEARCH is a versatile open-source tool for metagenomics.
vtk¶
- Homepage:
- Spack package:
- Versions:
- 8.0.1, 7.1.0, 7.0.0, 6.3.0, 6.1.0
- Build Dependencies:
- netcdf, libpng, hdf5, zlib, glew, opengl, qt, cmake, mesa, jsoncpp, libjpeg, libharu, lz4, freetype, netcdf-cxx, expat, libtiff, python, gl, libxml2
- Link Dependencies:
- netcdf, glew, hdf5, zlib, opengl, qt, mesa, libpng, jsoncpp, libjpeg, libharu, lz4, freetype, netcdf-cxx, expat, libtiff, python, gl, libxml2
- Description:
- The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization.
vtkh¶
- Homepage:
- Spack package:
- Versions:
- master
- Build Dependencies:
- cuda, cmake, mpi, tbb, vtkm
- Link Dependencies:
- cuda, cmake, mpi, tbb, vtkm
- Description:
- VTK-h is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-h brings together several projects like VTK-m and DIY2 to provide a toolkit with hybrid parallel capabilities.
vtkm¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0, master
- Build Dependencies:
- cuda, cmake, tbb
- Link Dependencies:
- cuda, cmake, tbb
- Description:
- VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.
wannier90¶
- Homepage:
- Spack package:
- Versions:
- 2.1.0, 2.0.1
- Build Dependencies:
- lapack, mpi, blas
- Link Dependencies:
- lapack, mpi, blas
- Description:
- Wannier90 calculates maximally-localised Wannier functions (MLWFs). Wannier90 is released under the GNU General Public License.
wget¶
- Homepage:
- Spack package:
- Versions:
- 1.19.1, 1.17, 1.16
- Build Dependencies:
- perl, libpsl, python, openssl, gettext, pkgconfig, zlib, pcre, gnutls
- Link Dependencies:
- zlib, libpsl, openssl, pcre, gnutls
- Description:
- GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non- interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
windowswmproto¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Description:
- This module provides the definition of the WindowsWM extension to the X11 protocol, used for coordination between an X11 server and the Microsoft Windows native window manager. WindowsWM is only intended to be used on Cygwin when running a rootless XWin server.
wt¶
- Homepage:
- Spack package:
- Versions:
- 3.3.7, master
- Build Dependencies:
- zlib, boost, sqlite, pango, openssl, mariadb, postgresql, cmake, libharu
- Link Dependencies:
- zlib, boost, sqlite, pango, openssl, mariadb, postgresql, libharu
- Description:
- Wt, C++ Web Toolkit. Wt is a C++ library for developing web applications.
wx¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.1.0, 3.0.2, 3.0.1
- Build Dependencies:
- pkgconfig, gtkplus
- Link Dependencies:
- gtkplus
- Description:
- wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature.
wxpropgrid¶
- Homepage:
- Spack package:
- Versions:
- 1.4.15
- Build Dependencies:
- wx
- Link Dependencies:
- wx
- Description:
- wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.
x11perf¶
- Homepage:
- Spack package:
- Versions:
- 1.6.0
- Build Dependencies:
- xproto, libxrender, libx11, util-macros, pkgconfig, libxmu, libxft
- Link Dependencies:
- libxmu, libxrender, libx11, libxft
- Description:
- Simple X server performance benchmarker.
xapian-core¶
- Homepage:
- Spack package:
- Versions:
- 1.4.3
- Build Dependencies:
- zlib
- Link Dependencies:
- zlib
- Description:
- Xapian is a highly adaptable toolkit which allows developers to easily add advanced indexing and search facilities to their own applications. It supports the Probabilistic Information Retrieval model and also supports a rich set of boolean query operators.
xauth¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- xproto, libx11, util-macros, libxext, pkgconfig, libxau, libxmu
- Link Dependencies:
- xproto, libxau, libxmu, libx11, libxext
- Description:
- The xauth program is used to edit and display the authorization information used in connecting to the X server.
xbacklight¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- pkgconfig, libxcb, util-macros, xcb-util
- Link Dependencies:
- libxcb, xcb-util
- Description:
- Xbacklight is used to adjust the backlight brightness where supported. It uses the RandR extension to find all outputs on the X server supporting backlight brightness control and changes them all in the same way.
xbiff¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- xbitmaps, libx11, util-macros, libxext, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxext, libxaw, libxmu, libx11
- Description:
- xbiff provides graphical notification of new e-mail. It only handles mail stored in a filesystem accessible file, not via IMAP, POP or other remote access protocols.
xbitmaps¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- The xbitmaps package contains bitmap images used by multiple applications built in Xorg.
xcalc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- xproto, libx11, util-macros, libxt, pkgconfig, libxaw
- Link Dependencies:
- libxaw, libx11, libxt
- Description:
- xcalc is a scientific calculator X11 client that can emulate a TI-30 or an HP-10C.
xcb-demo¶
- Homepage:
- Spack package:
- Versions:
- 0.1
- Build Dependencies:
- pkgconfig, xcb-util-wm, xcb-util-image, xcb-util, libxcb
- Link Dependencies:
- xcb-util-wm, xcb-util-image, xcb-util, libxcb
- Description:
- xcb-demo: A collection of demo programs that use the XCB library.
xcb-proto¶
- Homepage:
- Spack package:
- Versions:
- 1.12, 1.11
- Description:
- xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to generate the majority of its code and API.
xcb-util¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- pkgconfig, libxcb
- Link Dependencies:
- libxcb
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-cursor¶
- Homepage:
- Spack package:
- Versions:
- 0.1.3
- Build Dependencies:
- pkgconfig, xcb-util-renderutil, libxcb, xcb-util-image
- Link Dependencies:
- xcb-util-renderutil, libxcb, xcb-util-image
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-errors¶
- Homepage:
- Spack package:
- Versions:
- 1.0
- Build Dependencies:
- pkgconfig, xcb-proto, libxcb
- Link Dependencies:
- libxcb
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-image¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- pkgconfig, xproto, libxcb, xcb-util
- Link Dependencies:
- libxcb, xcb-util
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-keysyms¶
- Homepage:
- Spack package:
- Versions:
- 0.4.0
- Build Dependencies:
- pkgconfig, xproto, libxcb
- Link Dependencies:
- libxcb
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-renderutil¶
- Homepage:
- Spack package:
- Versions:
- 0.3.9
- Build Dependencies:
- pkgconfig, libxcb
- Link Dependencies:
- libxcb
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-wm¶
- Homepage:
- Spack package:
- Versions:
- 0.4.1
- Build Dependencies:
- pkgconfig, libxcb
- Link Dependencies:
- libxcb
- Description:
- The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.
xcb-util-xrm¶
- Homepage:
- Spack package:
- Versions:
- 1.2
- Build Dependencies:
- autoconf, m4, libtool, pkgconfig, automake, libxcb
- Link Dependencies:
- libxcb
- Description:
- XCB util-xrm module provides the 'xrm' library, i.e. utility functions for the X resource manager.
xclip¶
- Homepage:
- Spack package:
- Versions:
- 0.13
- Build Dependencies:
- autoconf, m4, libtool, automake, libxmu, libx11
- Link Dependencies:
- libxmu, libx11
- Description:
- xclip is a command line utility that is designed to run on any system with an X11 implementation. It provides an interface to X selections ("the clipboard") from the command line. It can read data from standard in or a file and place it in an X selection for pasting into other X applications. xclip can also print an X selection to standard out, which can then be redirected to a file or another program.
xclipboard¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- xproto, libx11, util-macros, libxt, pkgconfig, libxaw, libxkbfile, libxmu
- Link Dependencies:
- libxaw, libxkbfile, libxmu, libx11, libxt
- Description:
- xclipboard is used to collect and display text selections that are sent to the CLIPBOARD by other clients. It is typically used to save CLIPBOARD selections for later use. It stores each CLIPBOARD selection as a separate string, each of which can be selected.
xclock¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- xproto, libxrender, libxft, util-macros, libxt, pkgconfig, libxaw, libxkbfile, libxmu, libx11
- Link Dependencies:
- libxrender, libxft, libxt, libxaw, libxkbfile, libxmu, libx11
- Description:
- xclock is the classic X Window System clock utility. It displays the time in analog or digital form, continuously updated at a frequency which may be specified by the user.
xcmiscproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- XC-MISC Extension. This extension defines a protocol that provides Xlib two ways to query the server for available resource IDs.
xcmsdb¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- xcmsdb is used to load, query, or remove Device Color Characterization data stored in properties on the root window of the screen as specified in section 7, Device Color Characterization, of the X11 Inter-Client Communication Conventions Manual (ICCCM).
xcompmgr¶
- Homepage:
- Spack package:
- Versions:
- 1.1.7
- Build Dependencies:
- libxcomposite, libxrender, util-macros, libxext, libxfixes, pkgconfig, libxdamage
- Link Dependencies:
- libxfixes, libxcomposite, libxdamage, libxrender, libxext
- Description:
- xcompmgr is a sample compositing manager for X servers supporting the XFIXES, DAMAGE, RENDER, and COMPOSITE extensions. It enables basic eye- candy effects.
xconsole¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- xproto, libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- xproto, libxaw, libxmu, libx11, libxt
- Description:
- xconsole displays in a X11 window the messages which are usually sent to /dev/console.
xcursor-themes¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xcursorgen, libxcursor, util-macros
- Link Dependencies:
- libxcursor
- Description:
- This is a default set of cursor themes for use with libXcursor, originally created for the XFree86 Project, and now shipped as part of the X.Org software distribution.
xcursorgen¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- libpng, pkgconfig, libx11, util-macros, libxcursor
- Link Dependencies:
- libpng, libx11, libxcursor
- Description:
- xcursorgen prepares X11 cursor sets for use with libXcursor.
xdbedizzy¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- pkgconfig, libxext, libx11, util-macros
- Link Dependencies:
- libxext, libx11
- Description:
- xdbedizzy is a demo of the X11 Double Buffer Extension (DBE) creating a double buffered spinning scene.
xditview¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- xditview displays ditroff output on an X display.
xdm¶
- Homepage:
- Spack package:
- Versions:
- 1.1.11
- Build Dependencies:
- libxpm, libxt, pkgconfig, libxmu, libxext, libx11, util-macros, libxdmcp, libxau, libxinerama, libxaw, libxft
- Link Dependencies:
- libxinerama, libxext, libx11, libxt, libxpm, libxau, libxmu, libxaw, libxdmcp, libxft
- Description:
- X Display Manager / XDMCP server.
xdpyinfo¶
- Homepage:
- Spack package:
- Versions:
- 1.3.2
- Build Dependencies:
- libxext, libx11, recordproto, xproto, pkgconfig, libxtst, inputproto, libxcb, util-macros, fixesproto
- Link Dependencies:
- libxext, libx11, libxtst, libxcb
- Description:
- xdpyinfo is a utility for displaying information about an X server. It is used to examine the capabilities of a server, the predefined values for various parameters used in communicating between clients and the server, and the different types of screens, visuals, and X11 protocol extensions that are available.
xdriinfo¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- libxdamage, libx11, glproto, libxext, libxfixes, expat, pcre, pkgconfig, util-macros, libxshmfence
- Link Dependencies:
- libxdamage, libx11, libxext, libxfixes, expat, pcre, libxshmfence
- Description:
- xdriinfo - query configuration information of X11 DRI drivers.
xedit¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- Xedit is a simple text editor for X.
xerces-c¶
- Homepage:
- Spack package:
- Versions:
- 3.1.4
- Description:
- Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
xev¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, xproto, libxrandr, libx11, util-macros
- Link Dependencies:
- libxrandr, libx11
- Description:
- xev creates a window and then asks the X server to send it X11 events whenever anything happens to the window (such as it being moved, resized, typed in, clicked in, etc.). You can also attach it to an existing window. It is useful for seeing what causes events to occur and to display the information that they contain; it is essentially a debugging and development tool, and should not be needed in normal usage.
xextproto¶
- Homepage:
- Spack package:
- Versions:
- 7.3.0
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Protocol Extensions.
xeyes¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- libxext, libxrender, libx11, util-macros, libxt, pkgconfig, libxmu
- Link Dependencies:
- libxext, libxmu, libxrender, libx11, libxt
- Description:
- xeyes - a follow the mouse X demo, using the X SHAPE extension
xf86bigfontproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.0
- Description:
- X.org XF86BigFontProto protocol headers.
xf86dga¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libxxf86dga, pkgconfig, libx11, util-macros
- Link Dependencies:
- libxxf86dga, libx11
- Description:
- dga is a simple test client for the XFree86-DGA extension.
xf86dgaproto¶
- Homepage:
- Spack package:
- Versions:
- 2.1
- Description:
- X.org XF86DGAProto protocol headers.
xf86driproto¶
- Homepage:
- Spack package:
- Versions:
- 2.1.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- XFree86 Direct Rendering Infrastructure Extension. This extension defines a protocol to allow user applications to access the video hardware without requiring data to be passed through the X server.
xf86miscproto¶
- Homepage:
- Spack package:
- Versions:
- 0.9.3
- Description:
- This package includes the protocol definitions of the "XFree86-Misc" extension to the X11 protocol. The "XFree86-Misc" extension is supported by the XFree86 X server and versions of the Xorg X server prior to Xorg 1.6.
xf86rushproto¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Description:
- X.org XF86RushProto protocol headers.
xf86vidmodeproto¶
- Homepage:
- Spack package:
- Versions:
- 2.3.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- XFree86 Video Mode Extension. This extension defines a protocol for dynamically configuring modelines and gamma.
xfd¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- fontconfig, libxrender, libxft, util-macros, libxt, pkgconfig, libxaw, libxmu, xproto
- Link Dependencies:
- fontconfig, libxrender, libxft, libxt, libxaw, libxmu
- Description:
- xfd - display all the characters in a font using either the X11 core protocol or libXft2.
xfindproxy¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- xproto, util-macros, libxt, pkgconfig, xproxymanagementprotocol, libice
- Link Dependencies:
- libice, libxt
- Description:
- xfindproxy is used to locate available X11 proxy services. It utilizes the Proxy Management Protocol to communicate with a proxy manager. The proxy manager keeps track of all available proxy services, starts new proxies when necessary, and makes sure that proxies are shared whenever possible.
xfontsel¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- xfontsel application provides a simple way to display the X11 core protocol fonts known to your X server, examine samples of each, and retrieve the X Logical Font Description ("XLFD") full name for a font.
xfs¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- xproto, util-macros, pkgconfig, font-util, libxfont, xtrans, fontsproto
- Link Dependencies:
- font-util, libxfont
- Description:
- X Font Server.
xfsinfo¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, libfs, util-macros, xproto
- Link Dependencies:
- libfs
- Description:
- xfsinfo is a utility for displaying information about an X font server. It is used to examine the capabilities of a server, the predefined values for various parameters used in communicating between clients and the server, and the font catalogues and alternate servers that are available.
xfwp¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- pkgconfig, xproto, xproxymanagementprotocol, libice, util-macros
- Link Dependencies:
- libice
- Description:
- xfwp proxies X11 protocol connections, such as through a firewall.
xgamma¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros, libxxf86vm
- Link Dependencies:
- libx11, libxxf86vm
- Description:
- xgamma allows X users to query and alter the gamma correction of a monitor via the X video mode extension (XFree86-VidModeExtension).
xgc¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- util-macros, libxt, pkgconfig, libxaw, flex, bison
- Link Dependencies:
- libxaw, libxt
- Description:
- xgc is an X11 graphics demo that shows various features of the X11 core protocol graphics primitives.
xhost¶
- Homepage:
- Spack package:
- Versions:
- 1.0.7
- Build Dependencies:
- xproto, libx11, util-macros, pkgconfig, libxau, libxmu
- Link Dependencies:
- libxau, libxmu, libx11
- Description:
- xhost is used to manage the list of host names or user names allowed to make connections to the X server.
xineramaproto¶
- Homepage:
- Spack package:
- Versions:
- 1.2.1
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Xinerama Extension. This is an X extension that allows multiple physical screens controlled by a single X server to appear as a single screen.
xinit¶
- Homepage:
- Spack package:
- Versions:
- 1.3.4
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- The xinit program is used to start the X Window System server and a first client program on systems that are not using a display manager such as xdm.
xinput¶
- Homepage:
- Spack package:
- Versions:
- 1.6.2
- Build Dependencies:
- libxext, randrproto, libxrandr, libx11, util-macros, libxi, pkgconfig, libxinerama, xineramaproto, inputproto, fixesproto
- Link Dependencies:
- libxext, libxinerama, libxrandr, libx11, libxi
- Description:
- xinput is a utility to configure and test XInput devices.
xios¶
- Homepage:
- Spack package:
- Versions:
- develop, 1.0
- Build Dependencies:
- netcdf, perl, netcdf-fortran, boost, hdf5, mpi, perl-uri-escape, gmake, blitz
- Link Dependencies:
- netcdf, netcdf-fortran, boost, hdf5, mpi, blitz
- Description:
- XML-IO-SERVER library for IO management of climate models.
xkbcomp¶
- Homepage:
- Spack package:
- Versions:
- 1.3.1
- Build Dependencies:
- xproto, libx11, util-macros, pkgconfig, libxkbfile, bison
- Link Dependencies:
- libxkbfile, libx11
- Description:
- The X Keyboard (XKB) Extension essentially replaces the core protocol definition of a keyboard. The extension makes it possible to specify clearly and explicitly most aspects of keyboard behaviour on a per-key basis, and to track more closely the logical and physical state of a keyboard. It also includes a number of keyboard controls designed to make keyboards more accessible to people with physical impairments.
xkbdata¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- xkbcomp
- Description:
- The XKB data files for the various keyboard models, layouts, and locales.
xkbevd¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- pkgconfig, libxkbfile, bison, libx11, util-macros
- Link Dependencies:
- libxkbfile, libx11
- Description:
- XKB event daemon demo.
xkbprint¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libxkbfile, libx11, util-macros
- Link Dependencies:
- libxkbfile, libx11
- Description:
- xkbprint generates a printable or encapsulated PostScript description of an XKB keyboard description.
xkbutils¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- xproto, libx11, util-macros, libxt, pkgconfig, libxaw, inputproto
- Link Dependencies:
- libxaw, libx11, libxt
- Description:
- xkbutils is a collection of small utilities utilizing the XKeyboard (XKB) extension to the X11 protocol.
xkeyboard-config¶
- Homepage:
- Spack package:
- Versions:
- 2.18
- Build Dependencies:
- libxslt, pkgconfig, intltool, libx11, xproto
- Link Dependencies:
- libx11
- Description:
- This project provides a consistent, well-structured, frequently released, open source database of keyboard configuration data. The project is targeted to XKB-based systems.
xkill¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libxmu, libx11, util-macros
- Link Dependencies:
- libxmu, libx11
- Description:
- xkill is a utility for forcing the X server to close connections to clients. This program is very dangerous, but is useful for aborting programs that have displayed undesired windows on a user's screen.
xload¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- xproto, libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- xload displays a periodically updating histogram of the system load average.
xlogo¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- libxext, libxrender, libx11, libsm, libxt, pkgconfig, libxaw, libxmu, util-macros, libxft
- Link Dependencies:
- libxext, libxrender, libx11, libsm, libxt, libxaw, libxmu, libxft
- Description:
- The xlogo program simply displays the X Window System logo.
xlsatoms¶
- Homepage:
- Spack package:
- Versions:
- 1.1.2
- Build Dependencies:
- pkgconfig, libxcb, util-macros, libx11
- Link Dependencies:
- libxcb, libx11
- Description:
- xlsatoms lists the interned atoms defined on an X11 server.
xlsclients¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- pkgconfig, libxcb, util-macros, libx11
- Link Dependencies:
- libxcb, libx11
- Description:
- xlsclients is a utility for listing information about the client applications running on a X11 server.
xlsfonts¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- xlsfonts lists fonts available from an X server via the X11 core protocol.
xmag¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- xmag displays a magnified snapshot of a portion of an X11 screen.
xman¶
- Homepage:
- Spack package:
- Versions:
- 1.1.4
- Build Dependencies:
- pkgconfig, xproto, libxaw, util-macros, libxt
- Link Dependencies:
- libxaw, libxt
- Description:
- xman is a graphical manual page browser using the Athena Widgets (Xaw) toolkit.
xmessage¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, libxaw, util-macros, libxt
- Link Dependencies:
- libxaw, libxt
- Description:
- xmessage displays a message or query in a window. The user can click on an "okay" button to dismiss it or can select one of several buttons to answer a question. xmessage can also exit after a specified time.
xmh¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- xbitmaps, libx11, util-macros, libxt, pkgconfig, libxaw, libxmu
- Link Dependencies:
- libxaw, libxmu, libx11, libxt
- Description:
- The xmh program provides a graphical user interface to the MH Message Handling System. To actually do things with your mail, it makes calls to the MH package.
xmlf90¶
- Homepage:
- Spack package:
- Versions:
- 1.5.2
- Build Dependencies:
- automake, autoconf, m4, libtool
- Description:
- xmlf90 is a suite of libraries to handle XML in Fortran.
xmlto¶
- Homepage:
- Spack package:
- Versions:
- 0.0.28
- Build Dependencies:
- libxslt
- Link Dependencies:
- libxslt
- Description:
- Utility xmlto is a simple shell script for converting XML files to various formats. It serves as easy to use command line frontend to make fine output without remembering many long options and searching for the syntax of the backends.
xmodmap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.9
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- The xmodmap program is used to edit and display the keyboard modifier map and keymap table that are used by client applications to convert event keycodes into keysyms. It is usually run from the user's session startup script to configure the keyboard according to personal tastes.
xmore¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- pkgconfig, libxaw, util-macros, libxt
- Link Dependencies:
- libxaw, libxt
- Description:
- xmore - plain text display program for the X Window System.
xorg-cf-files¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- pkgconfig
- Description:
- The xorg-cf-files package contains the data files for the imake utility, defining the known settings for a wide variety of platforms (many of which have not been verified or tested in over a decade), and for many of the libraries formerly delivered in the X.Org monolithic releases.
xorg-docs¶
- Homepage:
- Spack package:
- Versions:
- 1.7.1
- Build Dependencies:
- pkgconfig, xmlto, util-macros, xorg-sgml-doctools
- Description:
- This package provides miscellaneous documentation for the X Window System that doesn't better fit into other packages. The preferred documentation format for these documents is DocBook XML.
xorg-gtest¶
- Homepage:
- Spack package:
- Versions:
- 0.7.1
- Build Dependencies:
- pkgconfig, libxi, libx11, util-macros, xorg-server
- Link Dependencies:
- libxi, libx11, xorg-server
- Description:
- Provides a Google Test environment for starting and stopping a X server for testing purposes.
xorg-server¶
- Homepage:
- Spack package:
- Versions:
- 1.18.99.901
- Build Dependencies:
- libdrm, glproto, flex, pkgconfig, font-util, bison, pixman, libx11, util-macros, dri2proto, dri3proto, libxshmfence
- Link Dependencies:
- libdrm, font-util, libxshmfence, pixman, libx11
- Description:
- X.Org Server is the free and open source implementation of the display server for the X Window System stewarded by the X.Org Foundation.
xorg-sgml-doctools¶
- Homepage:
- Spack package:
- Versions:
- 1.11
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- This package provides a common set of SGML entities and XML/CSS style sheets used in building/formatting the documentation provided in other X.Org packages.
xphelloworld¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- libxprintutil, libxprintapputil, libx11, util-macros, libxt, pkgconfig, libxaw, libxp
- Link Dependencies:
- libxprintutil, libxprintapputil, libx11, libxt, libxaw, libxp
- Description:
- Xprint sample applications.
xplor-nih¶
- Homepage:
- Spack package:
- Versions:
- 2.45
- Build Dependencies:
- python
- Run Dependencies:
- python
- Description:
- XPLOR-NIH is a structure determination program. Note: A manual download is required for XPLOR-NIH. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
xplsprinters¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, libxprintutil, libxp, libx11, util-macros
- Link Dependencies:
- libxprintutil, libxp, libx11
- Description:
- List Xprint printers.
xpr¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libxmu, libx11, util-macros
- Link Dependencies:
- libxmu, libx11
- Description:
- xpr takes as input a window dump file produced by xwd and formats it for output on various types of printers.
xprehashprinterlist¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, libxp, libx11, util-macros
- Link Dependencies:
- libxp, libx11
- Description:
- Rehash list of Xprint printers.
xprop¶
- Homepage:
- Spack package:
- Versions:
- 1.2.2
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- xprop is a command line tool to display and/or set window and font properties of an X server.
xproto¶
- Homepage:
- Spack package:
- Versions:
- 7.0.31, 7.0.29
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- X Window System Core Protocol. This package provides the headers and specification documents defining the X Window System Core Protocol, Version 11. It also includes a number of headers that aren't purely protocol related, but are depended upon by many other X Window System packages to provide common definitions and porting layer.
xproxymanagementprotocol¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Description:
- The Proxy Management Protocol is an ICE based protocol that provides a way for application servers to easily locate proxy services available to them.
xqilla¶
- Homepage:
- Spack package:
- Versions:
- 2.3.3
- Build Dependencies:
- xerces-c
- Link Dependencies:
- xerces-c
- Description:
- XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C library.
xrandr¶
- Homepage:
- Spack package:
- Versions:
- 1.5.0
- Build Dependencies:
- xproto, libxrender, libx11, libxrandr, pkgconfig, util-macros
- Link Dependencies:
- libxrender, libx11, libxrandr
- Description:
- xrandr - primitive command line interface to X11 Resize, Rotate, and Reflect (RandR) extension.
xrdb¶
- Homepage:
- Spack package:
- Versions:
- 1.1.0
- Build Dependencies:
- pkgconfig, xproto, libxmu, libx11, util-macros
- Link Dependencies:
- libxmu, libx11
- Description:
- xrdb - X server resource database utility.
xrefresh¶
- Homepage:
- Spack package:
- Versions:
- 1.0.5
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- xrefresh - refresh all or part of an X screen.
xrootd¶
- Homepage:
- Spack package:
- Versions:
- 4.6.0, 4.5.0, 4.4.1, 4.4.0, 4.3.0
- Build Dependencies:
- zlib, openssl, cmake
- Link Dependencies:
- zlib, openssl
- Description:
- The XROOTD project aims at giving high performance, scalable fault tolerant access to data repositories of many kinds.
xrx¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- libxext, libx11, util-macros, libxt, pkgconfig, libxau, libxaw, xproxymanagementprotocol, xtrans, libice
- Link Dependencies:
- libxext, libx11, libxt, libxau, libxaw, libice
- Description:
- The remote execution (RX) service specifies a MIME format for invoking applications remotely, for example via a World Wide Web browser. This RX format specifies a syntax for listing network services required by the application, for example an X display server. The requesting Web browser must identify specific instances of the services in the request to invoke the application.
xsbench¶
- Homepage:
- Spack package:
- Versions:
- 14, 13
- Build Dependencies:
- mpi
- Link Dependencies:
- mpi
- Description:
- XSBench is a mini-app representing a key computational kernel of the Monte Carlo neutronics application OpenMC. A full explanation of the theory and purpose of XSBench is provided in docs/XSBench_Theory.pdf.
xscope¶
- Homepage:
- Spack package:
- Versions:
- 1.4.1
- Build Dependencies:
- pkgconfig, xproto, xtrans, util-macros
- Description:
- XSCOPE -- a program to monitor X11/Client conversations.
xsdk¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.3.0, xsdk-0.2.0
- Build Dependencies:
- hypre, trilinos, petsc, pflotran, plasma, superlu-dist, alquimia, sundials, mfem, magma
- Link Dependencies:
- hypre, trilinos, petsc, pflotran, plasma, superlu-dist, alquimia, sundials, mfem, magma
- Description:
- Xsdk is a suite of Department of Energy (DOE) packages for numerical simulation. This is a Spack bundle package that installs the xSDK packages
xsdktrilinos¶
- Homepage:
- Spack package:
- Versions:
- develop, 12.8.1, 12.6.4, xsdk-0.2.0
- Build Dependencies:
- hypre, trilinos, petsc, mpi, cmake
- Link Dependencies:
- hypre, trilinos, petsc, mpi
- Description:
- xSDKTrilinos contains the portions of Trilinos that depend on PETSc because they would cause a circular dependency if built as part of Trilinos.
xset¶
- Homepage:
- Spack package:
- Versions:
- 1.2.3
- Build Dependencies:
- pkgconfig, xproto, libxmu, libx11, util-macros
- Link Dependencies:
- libxmu, libx11
- Description:
- User preference utility for X.
xsetmode¶
- Homepage:
- Spack package:
- Versions:
- 1.0.0
- Build Dependencies:
- pkgconfig, libxi, libx11, util-macros
- Link Dependencies:
- libxi, libx11
- Description:
- Set the mode for an X Input device.
xsetpointer¶
- Homepage:
- Spack package:
- Versions:
- 1.0.1
- Build Dependencies:
- pkgconfig, libxi, inputproto, libx11, util-macros
- Link Dependencies:
- libxi, libx11
- Description:
- Set an X Input device as the main pointer.
xsetroot¶
- Homepage:
- Spack package:
- Versions:
- 1.1.1
- Build Dependencies:
- xbitmaps, libx11, util-macros, xproto, pkgconfig, libxmu, libxcursor
- Link Dependencies:
- libxmu, libx11, libxcursor
- Description:
- xsetroot - root window parameter setting utility for X.
xsimd¶
- Homepage:
- Spack package:
- Versions:
- develop, 3.1.0
- Build Dependencies:
- cmake, googletest
- Link Dependencies:
- googletest
- Description:
- C++ wrappers for SIMD intrinsics
xsm¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libx11, libsm, libxt, pkgconfig, libxaw, libice, util-macros
- Link Dependencies:
- libice, libxaw, libx11, libsm, libxt
- Description:
- X Session Manager.
xstdcmap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- pkgconfig, xproto, libxmu, libx11, util-macros
- Link Dependencies:
- libxmu, libx11
- Description:
- The xstdcmap utility can be used to selectively define standard colormap properties. It is intended to be run from a user's X startup script to create standard colormap definitions in order to facilitate sharing of scarce colormap resources among clients using PseudoColor visuals.
xtensor¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.13.1
- Build Dependencies:
- cmake, xsimd, xtl
- Link Dependencies:
- xsimd, xtl
- Description:
- Multi-dimensional arrays with broadcasting and lazy computing
xterm¶
- Homepage:
- Spack package:
- Versions:
- 327
- Build Dependencies:
- fontconfig, libxpm, libxmu, libxt, libice, libxcb, libxext, libxrender, freetype, libxft, libsm, bzip2, libxau, libxinerama, libxaw, pkgconfig, libx11
- Link Dependencies:
- fontconfig, libxpm, libxmu, libxt, libice, libxext, libxrender, freetype, libxft, libsm, bzip2, libxau, libxinerama, libxaw, libxcb, libx11
- Description:
- The xterm program is a terminal emulator for the X Window System. It provides DEC VT102 and Tektronix 4014 compatible terminals for programs that can't use the window system directly.
xtl¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.3.4, 0.3.3
- Build Dependencies:
- cmake
- Description:
- QuantStack tools library
xtrans¶
- Homepage:
- Spack package:
- Versions:
- 1.3.5
- Build Dependencies:
- pkgconfig, util-macros
- Description:
- xtrans is a library of code that is shared among various X packages to handle network protocol transport in a modular fashion, allowing a single place to add new transport types. It is used by the X server, libX11, libICE, the X font server, and related components.
xtrap¶
- Homepage:
- Spack package:
- Versions:
- 1.0.2
- Build Dependencies:
- pkgconfig, libx11, util-macros, libxtrap
- Link Dependencies:
- libx11, libxtrap
- Description:
- XTrap sample clients.
xts¶
- Homepage:
- Spack package:
- Versions:
- 0.99.1
- Build Dependencies:
- libxi, perl, libxt, xset, libxmu, xtrans, xdpyinfo, libxext, mkfontdir, libx11, libxau, libxaw, libxtst, bdftopcf
- Link Dependencies:
- libxi, libx11, libxext, libxau, libxmu, libxt, libxaw, libxtst
- Description:
- This is a revamped version of X Test Suite (XTS) which removes some of the ugliness of building and running the tests.
xvidtune¶
- Homepage:
- Spack package:
- Versions:
- 1.0.3
- Build Dependencies:
- libx11, util-macros, libxt, pkgconfig, libxaw, libxmu, libxxf86vm
- Link Dependencies:
- libxaw, libxmu, libx11, libxxf86vm, libxt
- Description:
- xvidtune is a client interface to the X server video mode extension (XFree86-VidModeExtension).
xvinfo¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- pkgconfig, xproto, libxv, libx11, util-macros
- Link Dependencies:
- libxv, libx11
- Description:
- xvinfo prints out the capabilities of any video adaptors associated with the display that are accessible through the X-Video extension.
xwd¶
- Homepage:
- Spack package:
- Versions:
- 1.0.6
- Build Dependencies:
- pkgconfig, xproto, libxkbfile, libx11, util-macros
- Link Dependencies:
- libxkbfile, libx11
- Description:
- xwd - dump an image of an X window.
xwininfo¶
- Homepage:
- Spack package:
- Versions:
- 1.1.3
- Build Dependencies:
- pkgconfig, xproto, libxcb, util-macros, libx11
- Link Dependencies:
- libxcb, libx11
- Description:
- xwininfo prints information about windows on an X server. Various information is displayed depending on which options are selected.
xwud¶
- Homepage:
- Spack package:
- Versions:
- 1.0.4
- Build Dependencies:
- pkgconfig, xproto, libx11, util-macros
- Link Dependencies:
- libx11
- Description:
- xwud allows X users to display in a window an image saved in a specially formatted dump file, such as produced by xwd.
xz¶
- Homepage:
- Spack package:
- Versions:
- 5.2.3, 5.2.2, 5.2.0
- Description:
- XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.
yajl¶
- Homepage:
- Spack package:
- Versions:
- develop, 2.1.0
- Build Dependencies:
- cmake
- Description:
- Yet Another JSON Library (YAJL)
yaml-cpp¶
- Homepage:
- Spack package:
- Versions:
- develop, 0.5.3
- Build Dependencies:
- cmake, boost
- Link Dependencies:
- boost
- Description:
- A YAML parser and emitter in C++
yasm¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0
- Description:
- Yasm is a complete rewrite of the NASM-2.11.06 assembler. It supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes and outputs binary, ELF32 and ELF64 object formats.
yorick¶
- Homepage:
- Spack package:
- Versions:
- 2.2.04, master, f90-plugin
- Build Dependencies:
- libx11
- Link Dependencies:
- libx11
- Description:
- Yorick is an interpreted programming language for scientific simulations or calculations, postprocessing or steering large simulation codes, interactive scientific graphics, and reading, writing, or translating files of numbers. Yorick includes an interactive graphics package, and a binary file package capable of translating to and from the raw numeric formats of all modern computers. Yorick is written in ANSI C and runs on most operating systems (\*nix systems, MacOS X, Windows).
z3¶
- Homepage:
- Spack package:
- Versions:
- 4.5.0, 4.4.1, 4.4.0
- Build Dependencies:
- python
- Link Dependencies:
- python
- Description:
- Z3 is a theorem prover from Microsoft Research. It is licensed under the MIT license.
zeromq¶
- Homepage:
- Spack package:
- Versions:
- develop, 4.2.2, 4.1.4, 4.1.2, 4.1.1, 4.0.7, 4.0.6, 4.0.5
- Build Dependencies:
- pkgconfig, automake, autoconf, libtool, libsodium
- Link Dependencies:
- libsodium
- Description:
- The ZMQ networking/concurrency library and core API
zfp¶
- Homepage:
- Spack package:
- Versions:
- 0.5.1, 0.5.0
- Description:
- zfp is an open source C library for compressed floating-point arrays that supports very high throughput read and write random acces, target error bounds or bit rates. Although bit-for-bit lossless compression is not always possible, zfp is usually accurate to within machine epsilon in near-lossless mode, and is often orders of magnitude more accurate than other lossy compressors. Versions of zfp 0.5.1 or newer also support compression of integer data.
zip¶
- Homepage:
- Spack package:
- Versions:
- 3.0
- Build Dependencies:
- bzip2
- Link Dependencies:
- bzip2
- Description:
- Zip is a compression and file packaging/archive utility.
zlib¶
- Homepage:
- Spack package:
- Versions:
- 1.2.11, 1.2.8, 1.2.3
- Description:
- A free, general-purpose, legally unencumbered lossless data-compression library.
zoltan¶
- Homepage:
- Spack package:
- Versions:
- 3.83, 3.8, 3.6, 3.3
- Build Dependencies:
- mpi, parmetis
- Link Dependencies:
- mpi, parmetis
- Description:
- The Zoltan library is a toolkit of parallel combinatorial algorithms for parallel, unstructured, and/or adaptive scientific applications. Zoltan's largest component is a suite of dynamic load-balancing and paritioning algorithms that increase applications' parallel performance by reducing idle time. Zoltan also has graph coloring and graph ordering algorithms, which are useful in task schedulers and parallel preconditioners.
zsh¶
- Homepage:
- Spack package:
- Versions:
- 5.4.2, 5.3.1, 5.1.1
- Build Dependencies:
- ncurses, pcre
- Link Dependencies:
- ncurses, pcre
- Description:
- Zsh is a shell designed for interactive use, although it is also a powerful scripting language. Many of the useful features of bash, ksh, and tcsh were incorporated into zsh; many original features were added.
zstd¶
- Homepage:
- Spack package:
- Versions:
- 1.3.0, 1.1.2
- Description:
- Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.