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 mxnet r-corrplot
abyss nag r-covr
ack nalu r-cowplot
activeharmony namd r-crayon
adept-utils nano r-crosstalk
adios nanoflann r-cubature
adios2 nasm r-cubist
adlbx nauty r-curl
adol-c ncbi-rmblastn r-data-table
albert nccl r-dbi
alglib nccmp r-dbplyr
allinea-forge ncdu r-delayedarray
allinea-reports ncftp r-deldir
allpaths-lg ncl r-dendextend
alquimia nco r-deoptim
alsa-lib ncurses r-deoptimr
amg ncview r-deseq
amg2013 ndiff r-deseq2
amp nek5000 r-desolve
ampliconnoise nekbone r-devtools
amr-exp-parabolic nekcem r-diagrammer
amrex neovim r-dichromat
andi netcdf r-diffusionmap
angsd netcdf-cxx r-digest
ant netcdf-cxx4 r-diptest
antlr netcdf-fortran r-dnacopy
ape netgauge r-do-db
apex netgen r-domc
applewmproto netlib-lapack r-doparallel
appres netlib-scalapack r-dorng
apr netlib-xblas r-dose
apr-util nettle r-downloader
archer neuron r-dplyr
argp-standalone nextflow r-dt
argtable nfft r-dtw
arlecore nghttp2 r-dygraphs
armadillo nginx r-e1071
arpack-ng ngmlr r-edger
ascent ninja r-ellipse
asciidoc ninja-fortran r-ensembldb
aspa nlopt r-ergm
aspell nmap r-evaluate
aspell6-de nnvm r-expm
aspell6-en node-js r-factoextra
aspell6-es notmuch r-factominer
assimp npb r-ff
astra npm r-fftwtools
astral npth r-fgsea
astyle nspr r-filehash
atk numactl r-flashclust
atlas numdiff r-flexmix
atom-dft nut r-fnn
atompaw nwchem r-forcats
atop ocaml r-foreach
augustus oce r-forecast
autoconf oclint r-foreign
autodock-vina oclock r-formatr
autogen octave r-formula
automaded octave-optim r-fpc
automake octave-splines r-fracdiff
bamtools octave-struct r-futile-logger
bamutil octopus r-futile-options
barrnap of-adios-write r-gbm
bash ompss r-gcrma
bash-completion ompt-openmp r-gdata
bats oniguruma r-gdsfmt
bazel ont-albacore r-geiger
bbcp opa-psm2 r-genefilter
bbmap opam r-geneplotter
bcftools opari2 r-genomeinfodb
bcl2fastq2 openbabel r-genomeinfodbdata
bdftopcf openblas r-genomicalignments
bdw-gc opencoarrays r-genomicfeatures
bear opencv r-genomicranges
beast2 openexr r-geomorph
bedtools2 openfast r-geoquery
beforelight openfoam-com r-geosphere
benchmark openfoam-org r-getopt
berkeley-db openfst r-getoptlong
bertini opengl r-ggally
bib2xhtml openjpeg r-ggbio
bigreqsproto openmc r-ggdendro
binutils openmpi r-ggjoy
bioawk opennurbs r-ggmap
biopieces openscenegraph r-ggplot2
bison openspeedshop r-ggpubr
bitmap openssh r-ggrepel
blast-plus openssl r-ggridges
blat opium r-ggsci
blaze opus r-ggvis
bliss orfm r-gistr
blitz orthomcl r-git2r
bmake osu-micro-benchmarks r-glmnet
bml otf r-globaloptions
bohrium otf2 r-glue
boost p4est r-gmodels
boostmplcartesianproduct p7zip r-gmp
bowtie pacbio-daligner r-go-db
bowtie2 pacbio-damasker r-googlevis
boxlib pacbio-dazz-db r-gosemsim
bpp-core pacbio-dextractor r-gostats
bpp-phyl pagit r-gplots
bpp-seq pagmo r-graph
bpp-suite paml r-gridbase
braker panda r-gridextra
branson pandaseq r-gseabase
breakdancer pango r-gsubfn
breseq papi r-gtable
brigand paradiseo r-gtools
bsseeker2 parallel r-gtrellis
bucky parallel-netcdf r-gviz
busco paraver r-haven
butter paraview r-hexbin
bwa parmetis r-highr
byobu parmgridgen r-hmisc
bzip2 parsimonator r-hms
c-blosc parsplice r-htmltable
caffe partitionfinder r-htmltools
cairo patch r-htmlwidgets
caliper patchelf r-httpuv
callpath pathfinder r-httr
candle-benchmarks pax-utils r-hwriter
cantera pbmpi r-hypergraph
canu pcma r-ica
cap3 pcre r-igraph
cares pcre2 r-illuminaio
cask pdsh r-impute
casper pdt r-influencer
catalyst pegtl r-inline
catch pennant r-interactivedisplaybase
cbench percept r-ipred
cblas perl r-iranges
cbtf perl-algorithm-diff r-irdisplay
cbtf-argonavis perl-app-cmd r-irkernel
cbtf-argonavis-gui perl-array-utils r-irlba
cbtf-krell perl-b-hooks-endofscope r-iso
cbtf-lanl perl-bio-perl r-iterators
ccache perl-bit-vector r-janitor
cctools perl-capture-tiny r-jpeg
cdbfasta perl-carp-clan r-jsonlite
cdd perl-class-data-inheritable r-kegg-db
cddlib perl-class-inspector r-kegggraph
cdhit perl-class-load r-keggrest
cdo perl-class-load-xs r-kernlab
cereal perl-cpan-meta-check r-kernsmooth
cfitsio perl-data-optlist r-kknn
cgal perl-data-stag r-knitr
cgm perl-dbd-mysql r-labeling
cgns perl-dbfile r-lambda-r
charm perl-dbi r-laplacesdemon
check perl-devel-cycle r-lars
chlorop perl-devel-globaldestruction r-lattice
chombo perl-devel-overloadinfo r-latticeextra
cityhash perl-devel-stacktrace r-lava
clamr perl-digest-md5 r-lazyeval
cleaveland4 perl-dist-checkconflicts r-leaflet
cleverleaf perl-encode-locale r-leaps
clfft perl-eval-closure r-learnbayes
clhep perl-exception-class r-limma
clingo perl-exporter-tiny r-lme4
cloc perl-extutils-makemaker r-lmtest
cloog perl-extutils-pkgconfig r-locfit
cloverleaf perl-file-copy-recursive r-log4r
cloverleaf3d perl-file-listing r-lpsolve
clustalo perl-file-pushd r-lsei
clustalw perl-file-sharedir-install r-lubridate
cmake perl-file-slurp-tiny r-magic
cmocka perl-file-which r-magrittr
cmor perl-font-ttf r-makecdfenv
cnmem perl-gd r-maldiquant
cnpy perl-gd-graph r-mapproj
cns-nospec perl-gd-text r-maps
cntk perl-graph r-maptools
cntk1bitsgd perl-html-parser r-markdown
codar-cheetah perl-html-tagset r-mass
coevp perl-http-cookies r-matrix
cohmm perl-http-daemon r-matrixmodels
coinhsl perl-http-date r-matrixstats
comd perl-http-message r-mclust
compiz perl-http-negotiate r-mcmcglmm
compositeproto perl-inline r-mda
conduit perl-inline-c r-memoise
constype perl-intervaltree r-mergemaid
converge perl-io-html r-methodss3
coreutils perl-io-sessiondata r-mgcv
corset perl-io-socket-ssl r-mime
cosmomc perl-io-string r-minfi
cosp2 perl-list-moreutils r-minqa
cp2k perl-log-log4perl r-mixtools
cppad perl-lwp r-mlbench
cppcheck perl-lwp-mediatypes r-mlinterfaces
cpprestsdk perl-lwp-protocol-https r-mnormt
cppunit perl-math-cdf r-modelmetrics
cppzmq perl-module-build r-modelr
cram perl-module-runtime-conflicts r-modeltools
cryptopp perl-moose r-mpm
cscope perl-mozilla-ca r-msnbase
csdp perl-mro-compat r-multcomp
ctffind perl-namespace-clean r-multtest
cub perl-net-http r-munsell
cube perl-net-ssleay r-mvtnorm
cuda perl-package-deprecationmanager r-mzid
cuda-memtest perl-package-stash r-mzr
cudnn perl-package-stash-xs r-nanotime
cufflinks perl-padwalker r-ncbit
cups perl-params-util r-ncdf4
curl perl-parse-recdescent r-network
cvs perl-pdf-api2 r-networkd3
czmq perl-pegex r-nlme
dakota perl-perlio-gzip r-nloptr
daligner perl-soap-lite r-nmf
damageproto perl-star-fusion r-nnet
damselfly perl-statistics-descriptive r-nnls
darshan-runtime perl-sub-exporter r-nor1mix
darshan-util perl-sub-exporter-progressive r-np
dash perl-sub-identify r-numderiv
datamash perl-sub-install r-oligoclasses
dataspaces perl-sub-name r-oo
dbus perl-sub-uplevel r-openssl
dealii perl-svg r-org-hs-eg-db
dejagnu perl-swissknife r-organismdbi
delly2 perl-task-weaken r-packrat
denovogear perl-term-readkey r-pacman
dia perl-test-cleannamespaces r-pamr
dialign-tx perl-test-deep r-party
diamond perl-test-differences r-partykit
direnv perl-test-exception r-pathview
discovar perl-test-fatal r-pbapply
discovardenovo perl-test-memory-cycle r-pbdzmq
dlpack perl-test-most r-pbkrtest
dmlc-core perl-test-needs r-pcamethods
dmxproto perl-test-requires r-pcapp
docbook-xml perl-test-requiresinternet r-permute
docbook-xsl perl-test-warn r-pfam-db
dos2unix perl-test-warnings r-phantompeakqualtools
double-conversion perl-text-diff r-phyloseq
doxygen perl-text-unidecode r-pkgconfig
dri2proto perl-time-hires r-pkgmaker
dri3proto perl-time-piece r-plogr
dtcmp perl-try-tiny r-plotly
dyninst perl-uri r-plotrix
ea-utils perl-uri-escape r-pls
easybuild perl-version r-plyr
ebms perl-www-robotrules r-pmcmr
eccodes perl-xml-libxml r-png
ecp-proxy-apps perl-xml-parser r-prabclus
editres perl-xml-parser-lite r-praise
eigen perl-xml-simple r-preprocesscore
elemental perl-yaml-libyaml r-prettyunits
elfutils petsc r-prodlim
elk pexsi r-progress
elpa pfft r-protgenerics
emacs pflotran r-proto
emboss pfunit r-proxy
encodings pgdspider r-pryr
environment-modules pgi r-psych
es phantompeakqualtools r-ptw
esmf phasta r-purrr
espresso phylip r-quadprog
essl picard r-quantmod
ethminer pidx r-quantreg
etsf-io pigz r-quantro
everytrace piranha r-qvalue
everytrace-example pixman r-r6
evieext pkg-config r-randomforest
exabayes pkgconf r-ranger
exampm planck-likelihood r-rappdirs
exasp2 plasma r-raster
exmcutils plink r-rbgl
exodusii plumed r-rbokeh
exonerate pmgr-collective r-rcolorbrewer
expat pmix r-rcpp
expect pnfft r-rcpparmadillo
express pngwriter r-rcppcctz
extrae poamsa r-rcppeigen
exuberant-ctags pocl r-rcppprogress
f90cache polymake r-rcurl
falcon porta r-rda
farmhash portage r-readr
fastjar postgresql r-readxl
fastmath ppl r-registry
fastme prank r-rematch
fastphase presentproto r-reordercluster
fastq-screen preseq r-reportingtools
fastqc price r-repr
fastqvalidator primer3 r-reprex
fasttree printproto r-reshape
fastx-toolkit probconsrna r-reshape2
fenics prodigal r-rex
ferret proj r-rgdal
ffmpeg protobuf r-rgeos
fftw proxymngr r-rgl
fimpute pruners-ninja r-rgooglemaps
findutils ps-lite r-rgraphviz
fio psi4 r-rhdf5
fish pstreams r-rhtslib
fixesproto pugixml r-rinside
flac pumi r-rjags
flang pvm r-rjava
flann py-3to2 r-rjson
flash py-4suite-xml r-rjsonio
flecsale py-abipy r-rlang
flecsi py-adios r-rmarkdown
flex py-alabaster r-rminer
flint py-apache-libcloud r-rmpfr
flit py-apipkg r-rmpi
fltk py-appdirs r-rmysql
flux py-appnope r-rngtools
fmt py-apscheduler r-robustbase
foam-extend py-argcomplete r-rocr
folly py-argparse r-rodbc
font-adobe-100dpi py-ase r-roxygen2
font-adobe-75dpi py-asn1crypto r-rpart
font-adobe-utopia-100dpi py-astroid r-rpart-plot
font-adobe-utopia-75dpi py-astropy r-rpostgresql
font-adobe-utopia-type1 py-attrs r-rprojroot
font-alias py-autopep8 r-rsamtools
font-arabic-misc py-babel r-rsnns
font-bh-100dpi py-backports-abc r-rsqlite
font-bh-75dpi py-backports-functools-lru-cache r-rstan
font-bh-lucidatypewriter-100dpi py-backports-shutil-get-terminal-size r-rstudioapi
font-bh-lucidatypewriter-75dpi py-backports-ssl-match-hostname r-rtracklayer
font-bh-ttf py-basemap r-rtsne
font-bh-type1 py-beautifulsoup4 r-rvcheck
font-bitstream-100dpi py-binwalk r-rvest
font-bitstream-75dpi py-biom-format r-rzmq
font-bitstream-speedo py-biopython r-s4vectors
font-bitstream-type1 py-bitarray r-samr
font-cronyx-cyrillic py-bleach r-sandwich
font-cursor-misc py-blessings r-scales
font-daewoo-misc py-bokeh r-scatterplot3d
font-dec-misc py-boltons r-sdmtools
font-ibm-type1 py-bottleneck r-segmented
font-isas-misc py-brian r-selectr
font-jis-misc py-brian2 r-seqinr
font-micro-misc py-bsddb3 r-seurat
font-misc-cyrillic py-bx-python r-sfsmisc
font-misc-ethiopic py-cclib r-shape
font-misc-meltho py-cdat-lite r-shiny
font-misc-misc py-cdo r-shortread
font-mutt-misc py-certifi r-siggenes
font-schumacher-misc py-cffi r-simpleaffy
font-screen-cyrillic py-chardet r-sn
font-sony-misc py-click r-snow
font-sun-misc py-cogent r-snprelate
font-util py-colorama r-som
font-winitzki-cyrillic py-colormath r-somaticsignatures
font-xfree86-type1 py-configparser r-sourcetools
fontcacheproto py-counter r-sp
fontconfig py-coverage r-sparsem
fontsproto py-cpuinfo r-spdep
fonttosfnt py-cryptography r-speedglm
fpc py-csvkit r-sqldf
fr-hit py-current r-stanheaders
freebayes py-cutadapt r-statmod
freetype py-cycler r-statnet-common
fseq py-cython r-stringi
fsl py-dask r-stringr
fslsfonts py-dateutil r-strucchange
fstobdf py-dbf r-subplex
funhpc py-decorator r-summarizedexperiment
gapbs py-deeptools r-survey
gapcloser py-dendropy r-survival
gapfiller py-dev r-sva
gasnet py-dill r-tarifx
gatk py-dlcpar r-tclust
gaussian py-docutils r-tensora
gawk py-doxypy r-testit
gblocks py-doxypypy r-testthat
gcc py-dryscrape r-th-data
gccmakedep py-dxchange r-threejs
gccxml py-dxfile r-tibble
gconf py-easybuild-easyblocks r-tidycensus
gdal py-easybuild-easyconfigs r-tidyr
gdb py-easybuild-framework r-tiff
gdbm py-edffile r-tigris
gdk-pixbuf py-editdistance r-timedate
geant4 py-elasticsearch r-topgo
gearshifft py-elephant r-trimcluster
gemmlowp py-emcee r-trust
genemark-et py-entrypoints r-tseries
genometools py-enum34 r-tsne
geos py-epydoc r-ttr
gettext py-espresso r-udunits2
gflags py-espressopp r-units
ghostscript py-et-xmlfile r-utils
ghostscript-fonts py-execnet r-uuid
giflib py-fastaindex r-variantannotation
git py-fasteners r-varselrf
git-lfs py-faststructure r-vcd
gl2ps py-fiscalyear r-vegan
glew py-flake8 r-vgam
glib py-flask r-viridis
glm py-flexx r-viridislite
global py-fparser r-visnetwork
globalarrays py-funcsigs r-vsn
globus-toolkit py-functools32 r-whisker
glog py-future r-withr
glpk py-futures r-xde
glproto py-genders r-xgboost
gmake py-genshi r-xlconnect
gmap-gsnap py-git-review r-xlconnectjars
gmime py-git2 r-xlsx
gmp py-gnuplot r-xlsxjars
gmsh py-griddataformats r-xmapbridge
gnat py-guidata r-xml
gnu-prolog py-guiqwt r-xml2
gnupg py-h5py r-xtable
gnuplot py-html2text r-xts
gnutls py-html5lib r-xvector
go py-htseq r-yaml
go-bootstrap py-httpbin r-yapsa
gobject-introspection py-hypothesis r-yaqcaffy
googletest py-idna r-yarn
gotcha py-igraph r-zlibbioc
gource py-imagesize r-zoo
gperf py-iminuit raft
gperftools py-importlib raja
grackle py-ipaddress randfold
gradle py-ipdb random123
grandr py-ipykernel randrproto
graphlib py-ipython ravel
graphmap py-ipython-genutils raxml
graphviz py-ipywidgets ray
grib-api py-isort rdp-classifier
groff py-itsdangerous re2c
gromacs py-jdcal readline
gsl py-jedi recordproto
gslib py-jinja2 redundans
gtkorvo-atl py-joblib relion
gtkorvo-cercs-env py-jpype rempi
gtkorvo-dill py-jsonschema rename
gtkorvo-enet py-junit-xml rendercheck
gtkplus py-jupyter-client renderproto
gts py-jupyter-console repeatmasker
guidance py-jupyter-core resourceproto
guile py-jupyter-notebook revbayes
h5hut py-keras rgb
h5part py-latexcodec rhash
h5utils py-lazy rlwrap
h5z-zfp py-lazy-object-proxy rmlab
hacckernels py-lazyarray rna-seqc
hadoop py-libconf rockstar
hapcut2 py-libensemble root
haploview py-line-profiler rose
harfbuzz py-linecache2 rr
harminv py-lit rsbench
hdf py-llvmlite rsem
hdf5 py-lmfit rstart
hdf5-blosc py-localcider rsync
help2man py-lockfile rtags
hepmc py-logilab-common rtax
heppdt py-lrudict ruby
highfive py-lxml ruby-gnuplot
highwayhash py-lzstring ruby-narray
hisat2 py-macholib ruby-rubyinline
hmmer py-machotools ruby-terminal-table
hoomd-blue py-macs2 rust
hpccg py-mako rust-bindgen
hpctoolkit py-mappy sabre
hpctoolkit-externals py-markdown sailfish
hpgmg py-markupsafe salmon
hpl py-matplotlib sambamba
hpx py-mccabe samblaster
hpx5 py-mdanalysis samrai
hsakmt py-meep samtools
hstr py-memory-profiler sandbox
htop py-methylcode sas
htslib py-misopy satsuma2
httpie py-mistune savanna
hub py-mock saws
hunspell py-moltemplate sbt
hwloc py-mongo scala
hybpiper py-monotonic scalasca
hydra py-monty scalpel
hypre py-mpi4py scan-for-matches
i3 py-mpmath scons
ibmisc py-multiprocess scorec-core
iceauth py-multiqc scorep
icedtea py-mx scotch
icet py-mxnet scr
ico py-myhdl screen
icu4c py-mysqldb1 scripts
id3lib py-nbconvert scrnsaverproto
idba py-nbformat sctk
igraph py-neo sdl2
igv py-nestle sdl2-image
ilmbase py-netcdf4 sed
image-magick py-netifaces seqprep
imake py-networkx seqtk
impute2 py-nose serf
infernal py-nosexcover sessreg
inputproto py-numba setxkbmap
intel py-numexpr sga
intel-daal py-numpy shapeit
intel-gpu-tools py-numpydoc shared-mime-info
intel-ipp py-olefile shiny-server
intel-mkl py-ont-fast5-api shortstack
intel-mkl-dnn py-openpmd-validator showfont
intel-mpi py-openpyxl sickle
intel-parallel-studio py-ordereddict siesta
intel-tbb py-oset signalp
intltool py-packaging signify
ior py-palettable silo
iozone py-pandas simplemoc
ipopt py-paramiko simul
isaac py-pathlib2 simulationio
isaac-server py-pathos singularity
isl py-pathspec slepc
itstool py-patsy slurm
itsx py-pbr smalt
jags py-periodictable smc
jansson py-petsc4py smproxy
jasper py-pexpect snakemake
jbigkit py-phonopy snap
jdk py-pickleshare snap-berkeley
jellyfish py-pil snap-korf
jemalloc py-pillow snappy
jmol py-pip snbone
jq py-pipits sniffles
json-c py-pkgconfig snptest
json-cwx py-plotly soap2
json-glib py-ply soapindel
jsoncpp py-pmw soapsnp
judy py-pox somatic-sniper
julia py-ppft sortmerna
kahip py-prettytable sosflow
kaks-calculator py-proj sowing
kaldi py-prompt-toolkit sox
kallisto py-protobuf spades
kbproto py-psutil spark
kdiff3 py-psyclone sparsehash
kealib py-ptyprocess sparta
kentutils py-pudb spdlog
kmergenie py-py spectrum-mpi
kokkos py-py2bit speex
kraken py-py2cairo sph2pipe
krims py-py2neo spherepack
kripke py-py4j spindle
kvasir-mpl py-pyani spot
laghos py-pyasn1 sqlite
lammps py-pybedtools squid
last py-pybigwig sra-toolkit
latte py-pybind11 sspace-longread
launchmon py-pybtex sspace-standard
lazyten py-pybtex-docutils sst-dumpi
lbann py-pychecker sst-macro
lbxproxy py-pycodestyle stacks
lcals py-pycparser staden-io-lib
lcms py-pycrypto star
ldc py-pycurl star-ccm-plus
ldc-bootstrap py-pydatalog startup-notification
legion py-pydispatcher stat
leveldb py-pydot stc
lftp py-pyelftools stream
libaec py-pyfasta strelka
libaio py-pyfftw stress
libapplewm py-pyflakes stringtie
libarchive py-pygments structure
libassuan py-pygobject sublime-text
libatomic-ops py-pygtk subread
libbeagle py-pylint subversion
libbsd py-pymatgen suite-sparse
libbson py-pyminifier sumaclust
libcanberra py-pympler sundials
libcap py-pynn superlu
libcerf py-pypar superlu-dist
libcint py-pyparsing superlu-mt
libcircle py-pypeflow sw4lite
libconfig py-pyprof2html swarm
libcroco py-pyqt swfft
libctl py-pyrad swiftsim
libdivsufsort py-pysam swig
libdmx py-pyscaf symengine
libdrm py-pyserial sympol
libdwarf py-pyside sz
libedit py-pysocks tabix
libelf py-pytables talloc
libemos py-pytest tantan
libepoxy py-pytest-cov tar
libev py-pytest-flake8 targetp
libevent py-pytest-httpbin task
libevpath py-pytest-mock taskd
libfabric py-pytest-runner tasmanian
libffi py-pytest-xdist tassel
libffs py-python-daemon tau
libfontenc py-python-gitlab tcl
libfs py-pythonqwt tcoffee
libgcrypt py-pytz tcsh
libgd py-pywavelets tealeaf
libgit2 py-pyyaml tetgen
libgpg-error py-qtawesome tethex
libgpuarray py-qtconsole texinfo
libgridxc py-qtpy texlive
libgtextutils py-quantities the-platinum-searcher
libharu py-radical-utils the-silver-searcher
libhio py-ranger thrift
libice py-readme-renderer thrust
libiconv py-regex tig
libint py-reportlab tinyxml
libjpeg py-requests tinyxml2
libjpeg-turbo py-restview tioga
libksba py-rope tk
liblbxutil py-rpy2 tmalign
libmatheval py-rsa tmhmm
libmesh py-rseqc tmux
libmng py-rtree tmuxinator
libmongoc py-saga-python tophat
libmonitor py-scandir tppred
libnbc py-scientificpython transabyss
libogg py-scikit-image transdecoder
liboldx py-scikit-learn transposome
libpcap py-scipy transset
libpciaccess py-seaborn trapproto
libpfm4 py-setuptools tree
libpipeline py-setuptools-git trf
libpng py-setuptools-scm triangle
libpsl py-sfepy trilinos
libpthread-stubs py-sh trimgalore
libquo py-shiboken trimmomatic
libsigsegv py-simplegeneric turbine
libsm py-simplejson turbomole
libsodium py-singledispatch tut
libspatialindex py-sip twm
libsplash py-six tycho2
libssh2 py-slepc4py typhonio
libsvm py-sncosmo uberftp
libszip py-snowballstemmer ucx
libtermkey py-spectra udunits2
libtiff py-spefile ufo-core
libtool py-spglib ufo-filters
libunistring py-sphinx unblur
libunwind py-sphinx-bootstrap-theme uncrustify
libuuid py-sphinx-rtd-theme unibilium
libuv py-sphinxcontrib-bibtex unison
libvorbis py-sphinxcontrib-programoutput units
libvterm py-sphinxcontrib-websupport unixodbc
libwebsockets py-spyder usearch
libwindowswm py-spykeutils util-linux
libx11 py-sqlalchemy util-macros
libxau py-statsmodels uuid
libxaw py-storm valgrind
libxaw3d py-subprocess32 vampirtrace
libxc py-symengine vardictjava
libxcb py-symfit varscan
libxcomposite py-sympy vc
libxcursor py-tabulate vcftools
libxdamage py-tappy vcsh
libxdmcp py-terminado vdt
libxevie py-tetoolkit vecgeom
libxext py-theano veclibfort
libxfixes py-tifffile vegas2
libxfont py-toml velvet
libxfont2 py-tomopy videoproto
libxfontcache py-tornado viennarna
libxft py-tqdm viewres
libxi py-traceback2 vim
libxinerama py-traitlets virtualgl
libxkbcommon py-tuiview visit
libxkbfile py-twisted vizglow
libxkbui py-typing vmatch
libxml2 py-tzlocal voropp
libxmu py-umi-tools votca-csg
libxp py-unittest2 votca-ctp
libxpm py-unittest2py3k votca-moo
libxpresent py-urllib3 votca-tools
libxprintapputil py-urwid votca-xtp
libxprintutil py-vcversioner vpfft
libxrandr py-virtualenv vpic
libxrender py-vsc-base vsearch
libxres py-vsc-install vtk
libxscrnsaver py-wcsaxes vtkh
libxshmfence py-wcwidth vtkm
libxslt py-webkit-server wannier90
libxsmm py-werkzeug wget
libxstream py-wheel windowswmproto
libxt py-widgetsnbextension wt
libxtrap py-wrapt wx
libxtst py-xarray wxpropgrid
libxv py-xattr x11perf
libxvmc py-xlrd xapian-core
libxxf86dga py-xlsxwriter xauth
libxxf86misc py-xmlrunner xbacklight
libxxf86vm py-xopen xbiff
libyogrt py-xpyb xbitmaps
libzip py-xvfbwrapper xcalc
likwid py-yapf xcb-demo
linkphase3 py-yt xcb-proto
linux-headers py-zmq xcb-util
listres python xcb-util-cursor
llvm qbank xcb-util-errors
llvm-lld qbox xcb-util-image
llvm-openmp-ompt qhull xcb-util-keysyms
lmdb qmcpack xcb-util-renderutil
lmod qmd-progress xcb-util-wm
lndir qrupdate xcb-util-xrm
log4cplus qt xclip
log4cxx qt-creator xclipboard
lrslib qtgraph xclock
lrzip qthreads xcmiscproto
lua quinoa xcmsdb
lua-bitlib qwt xcompmgr
lua-jit r xconsole
lua-lpeg r-a4 xcursor-themes
lua-luafilesystem r-a4base xcursorgen
lua-luaposix r-a4classif xdbedizzy
lua-mpack r-a4core xditview
luit r-a4preproc xdm
lulesh r-a4reporting xdpyinfo
lumpy-sv r-abadata xdriinfo
lwgrp r-abaenrichment xedit
lwm2 r-abind xerces-c
lz4 r-absseq xev
lzma r-acde xextproto
lzo r-acepack xeyes
m4 r-acgh xf86bigfontproto
macsio r-acme xf86dga
mad-numdiff r-ada xf86dgaproto
mafft r-adabag xf86driproto
magics r-ade4 xf86miscproto
magma r-adegenet xf86rushproto
makedepend r-adsplit xf86vidmodeproto
mallocmc r-affxparser xfd
man-db r-affy xfindproxy
maq r-affycomp xfontsel
mariadb r-affycompatible xfs
masa r-affycontam xfsinfo
masurca r-affycoretools xfwp
matio r-affydata xgamma
matlab r-affyexpress xgc
maven r-affyilm xhost
maverick r-affyio xineramaproto
mawk r-affypdnn xinit
mbedtls r-affyplm xinput
mcl r-affyqcreport xios
mdtest r-affyrnadegradation xkbcomp
meep r-agdex xkbdata
mefit r-agilp xkbevd
memaxes r-agimicrorna xkbprint
meme r-aims xkbutils
meraculous r-aldex2 xkeyboard-config
mercurial r-allelicimbalance xkill
mesa r-alpine xload
mesa-glu r-als xlogo
meshkit r-alsace xlsatoms
meson r-altcdfenvs xlsclients
mesquite r-ampliqueso xlsfonts
metaphysicl r-analysispageserver xmag
metasv r-anaquin xman
metis r-aneufinder xmessage
mfem r-aneufinderdata xmh
microbiomeutil r-annaffy xmlf90
minced r-annotate xmlto
miniaero r-annotationdbi xmodmap
miniamr r-annotationfilter xmore
miniconda2 r-annotationforge xorg-cf-files
miniconda3 r-annotationhub xorg-docs
minife r-ape xorg-gtest
minighost r-assertthat xorg-server
minigmg r-backports xorg-sgml-doctools
minimap2 r-bamsignals xphelloworld
minimd r-base64 xplor-nih
miniqmc r-base64enc xplsprinters
minisign r-beanplot xpr
minismac2d r-bh xprehashprinterlist
minitri r-bindr xprop
minixyce r-bindrcpp xproto
mira r-biobase xproxymanagementprotocol
mirdeep r-biocgenerics xqilla
mitofates r-biocinstaller xrandr
mitos r-biocparallel xrdb
mkfontdir r-biocstyle xrefresh
mkfontscale r-biomart xrootd
mlhka r-biomformat xrx
moab r-biostrings xsbench
molcas r-biovizbase xscope
mono r-bit xsdk
mosh r-bit64 xsdktrilinos
mothur r-bitops xset
motif r-blob xsetmode
motioncor2 r-bookdown xsetpointer
mozjs r-boot xsetroot
mpc r-brew xsimd
mpe2 r-broom xsm
mpest r-bsgenome xstdcmap
mpfr r-bumphunter xtensor
mpibash r-c50 xterm
mpiblast r-callr xtl
mpich r-car xtrans
mpifileutils r-caret xtrap
mpileaks r-category xts
mpip r-catools xvidtune
mpir r-cellranger xvinfo
mpix-launch-swift r-checkmate xwd
mrbayes r-checkpoint xwininfo
mrnet r-chemometrics xwud
mrtrix3 r-chron xz
msgpack-c r-circlize yajl
mshadow r-class yaml-cpp
multitail r-classint yasm
multiverso r-cli yorick
mummer r-clipr z3
mumps r-cluster zeromq
munge r-clusterprofiler zfp
muparser r-coda zip
muscle r-codetools zlib
muse r-coin zoltan
muster r-colorspace zsh
mvapich2 r-complexheatmap zstd
mxml r-corpcor None

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

Homepage:
Spack package:
Versions:
1.6.2, 1.5.2
Description:
Apache portable runtime.

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.

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

blitz

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0
Description:
N-dimensional arrays for C++

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-argonavis

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
cuda, boost, papi, cmake, cbtf-krell, cbtf, mrnet
Link Dependencies:
cuda, boost, papi, cbtf-krell, cbtf, mrnet
Description:
CBTF Argo Navis project contains the CUDA collector and supporting libraries that was done as a result of a DOE SBIR grant.

cbtf-argonavis-gui

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
openspeedshop, qtgraph, qt, cmake, xerces-c, mrnet, cuda, boost, cbtf-argonavis, graphviz, cbtf-krell, cbtf
Link Dependencies:
cuda, cbtf, openspeedshop, boost, cbtf-argonavis, graphviz, qtgraph, qt, cbtf-krell, xerces-c, mrnet
Description:
CBTF Argo Navis GUI project contains the GUI that views OpenSpeedShop performance information by loading in the Sqlite database files.

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

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-xml

Homepage:
Spack package:
Versions:
4.5
Description:
Docbook DTD XML files.

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

exuberant-ctags

Homepage:
Spack package:
Versions:
5.8
Description:
The canonical ctags generator

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.

ghostscript-fonts

Homepage:
Spack package:
Versions:
8.11
Description:
Ghostscript Fonts

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.

kvasir-mpl

Homepage:
Spack package:
Versions:
develop
Description:
Kvasir metaprogramming library

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.

libgtextutils

Homepage:
Spack package:
Versions:
0.7
Description:
Gordon's Text utils Library.

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.

libspatialindex

Homepage:
Spack package:
Versions:
1.8.5
Build Dependencies:
cmake
Description:

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.

libuuid

Homepage:
Spack package:
Versions:
1.0.3
Description:
Portable uuid C library

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.

linux-headers

Homepage:
Spack package:
Versions:
4.9.10
Description:
The Linux kernel headers.

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-jit

Homepage:
Spack package:
Versions:
2.0.4
Description:
Flast flexible JITed 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

muparser

Homepage:
Spack package:
Versions:
2.2.5
Description:
C++ math expression parser library.

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.

muse

Homepage:
Spack package:
Versions:
1.0-rc
Description:
Somatic point mutation caller.

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.

nag

Homepage:
Spack package:
Versions:
6.1, 6.0
Description:
The NAG Fortran Compiler.

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.

oniguruma

Homepage:
Spack package:
Versions:
6.1.3
Description:
Regular expression library.

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

p7zip

Homepage:
Spack package:
Versions:
16.02
Description:
A Unix port of the 7z file archiver

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-sharedir-install

Homepage:
Spack package:
Versions:
0.11
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Install shared files

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-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-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-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.

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-pickleshare

Homepage:
Spack package:
Versions:
0.7.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Tiny 'shelve'-like database with concurrency support

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-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-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-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-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-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-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-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-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-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.

shared-mime-info

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
pkgconfig, libxml2, glib, gettext, intltool
Link Dependencies:
glib, libxml2
Description:
Database of common MIME types.

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

spectrum-mpi

Homepage:
Spack package:
Description:
IBM MPI implementation from Spectrum MPI.

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.

trapproto

Homepage:
Spack package:
Versions:
3.4.3
Description:
X.org TrapProto protocol headers.

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.

unibilium

Homepage:
Spack package:
Versions:
1.2.0
Description:
A terminfo parsing library

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.

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.