Software that has been successfully used on SHIROKANE

General Freeware

a2ps
AGREP
AMBER
Anaconda
Ant
APR
APR-util
ATK
ATLAS
AT-SPI2
Autoconf
AutoGen
Automake
BerkeleyDB
Binutils
Bison
BLAS
Boost
bzip2
Cairo
Cairomm
c-blosc
ccache
cdb
CLISP
CLooG
CMake
cURL
CVS
DBus
DBus-GLib
DDD
DejaGnu
Diffutils
DocBook-utils
Doxygen
Eclipse
Eigen
Emacs
Expat
Expect
FANN
FFmpeg
FFTW
fileutils
findutils
Flex
fmirror
Fontconfig
FreeType
FreeWnn
GCC
GConf
GDB
GDK-PixBuf
gettext
GHC
Ghostscript
Git
GLib
GLibmm
Glimpse
GlobusToolkit
GLPK
GMP
GnuPG
Gnuplot
google-sparsehash
gperf
GraphicsMagick
Graphviz
grep
GROMACS
GSL
GTK+
Guile
HarfBuzz
HDF5
HPN-SSH
HSCP
igraph
ImageJ
ImageMagick
Inkscape
isl
Ispell
Java
Julia
LAM
LAPACK
LAPACK++
LaTeX
LFTP
libbonobo
libbzip2
libcanberra
libevent
libffi
libgsf
libiconv
libIDL
libjpeg
libogg
libpng
LibreOffice
librsync
libsigc++
libsodium
libstatgrab
libtiff
Libtool
libungif
libunistring
libvorbis
libxml2
libXpm
libyaml
LittleCMS
Lua
LV
Lynx
LZ4
M4
Make
MATLAB_Compiler_Runtime
matrix-toolkits-java
Mercurial
Mew
mgzip
MH
MolScript
MongoDB
MPC
MPFR
MPICH
MPICH2
mpiJava
MySQL
NcFTP
ncurses
NetCDF
netlib-java
nkf
Node.js
Octave
OpenBabel
OpenCV
OpenJPEG
OpenMotif
OpenMPI
OpenSlide
OpenSSL
ORBit2
P7ZIP
Pango
Pangomm
Parallel
PBZIP2
PCRE
pdsh
Perl
PHP
Pixman
pkg-config
plotutils
POPT
PostgreSQL
POV-Ray
PPL
Python
Qt
R
Readline
RLPR
RStudio
RStudio Desktop
rsync
Ruby
SBCL
screen
Serf
Singularity
SoX
SQLite
STLport
Subversion
SUNDIALS
SVN
SWIG
tar
Tcl
teTex
Texinfo
Tk
tmux
tree
VIPS
wget
Xerces-C++
XQilla
XZ_Utils
Yasm
ZeroMQ
zlib

Bio Freeware

ABySS
ALSCRIPT
AmberTools
APT
ARCS
AUGUSTUS
BamTools
bcl2fastq
BCL2FASTQ
BEAGLE
BEAST
BEDTools
biobambam2
Bioconductor
Biopieces
Bioscope
BLAST
BLAST+
BLAT
Bowtie
Bowtie2
BWA
Canu
CAP3
CD-HIT
Circos
ClustalW
COPASI
CREAD
Cufflinks
Cytoscape
Darn
DIAMOND
DROMPA
EMBOSS
Exonerate
eXpress
FALCON
FasnQC
FasnTree
FASTA
FastML
FastQC
FastTree
FASTX-Toolkit
FreeBayes
GENESIS
GeneTorrent
GMAP
HISAT
HISAT2
HMMER
IgBLAST
IGV
InterProScan
io_lib
Ion-Variant-Hunter
Jellyfish
JGAP
Juicer
Karn
kClust
libGTextUtils
libsequence
lobSTR
MAFFT
Maq
MATLAB
MCL
MEGAHIT
MEME
MEME Suite
Meta-MEME
Minimap
MMseqs
MolScript
MUMmer
NCBI_Toolkit
NCBI-CXX-Toolkin
NEURON
NovoAlign
ORFfinder
PASA
PGENESIS
PHYLIP
phyx
Picard
Platanus
Polysolver
PRANK
Prodigal
RasMol
Raster3D
RAxML
Roary
Salmon
SAMtools
SEER
SICER
SnpEff
SnringTie
SOAPdenovo
SOAPdenovo2
SPAdes
SRA
SRA-Toolkin
SSAKE
STAR
StochKit
StringTie
Tandem_Repeats_Finder
TMAP
TopHat
Torrent_Variant_Caller
TorrentSuite
TRF
Trinity
VariationHunter
VCFtools
Velven
Velvet
VelvetOptimiser
vidjil-algo
VMD
VSEARCH

R modules

abind
acepack
ade4
affy
affydata
affyio
affyPLM
affyQCReport
akima
annaffy
annotate
AnnotationDbi
AnnotationForge
AnnotationHub
ape
askpass
assertthat
ath1121501cdf
ath1121501probe
backports
base
base64enc
BatchJobs
baySeq
BBmisc
beanplot
BH
BiasedUrn
Biobase
BiocGenerics
BiocInstaller
BiocParallel
biomaRt
Biostrings
bitops
BMA
boot
brew
BSgenome
callr
Category
caTools
checkmate
ChIPpeakAnno
chron
class
cli
clipr
clisymbols
cluster
codetools
coloc
colorspace
compiler
crayon
curl
datasets
DBI
DEoptimR
desc
DESeq
DESeq2
devtools
dichromat
digest
dplyr
DPpackage
dynamicTreeCut
DynDoc
edgeR
ensembldb
evaluate
fail
fansi
fields
flashClust
foreach
foreign
formatR
Formula
fpc
fs
gcrma
gdata
gee
genefilter
geneLenDataBase
geneplotter
GenomeInfoDb
GenomicAlignments
GenomicFeatures
GenomicRanges
ggplot2
gh
git2r
glmmML
glue
gmodels
goseq
GOstats
gplots
graph
graphics
grDevices
grid
gridExtra
GSEABase
gsubfn
gtable
gtools
hexbin
hgu133plus2cdf
hiAnnotator
highr
Hmisc
htmltools
htmlwidgets
httpuv
httr
hwriter
idr
impute
ini
inline
IRanges
iterators
itertools
jsonlite
KernSmooth
knitr
labeling
lattice
latticeExtra
lazy
lazyeval
leaps
limma
lme4
locfit
magrittr
maps
markdown
marray
MASS
Matrix
MatrixModels
matrixStats
mclust
memoise
methods
mgcv
mime
minqa
mouse4302cdf
multcomp
multtest
munsell
mvtnorm
nlme
nloptr
nnet
openssl
parallel
pcaPP
PEER
perm
pillar
pkgbuild
pkgconfig
pkgload
plyr
polspline
preprocessCore
prettyunits
processx
proto
ps
purrr
quantreg
R6
rae230acdf
rat2302cdf
RBGL
rcmdcheck
RColorBrewer
Rcpp
RcppArmadillo
RcppEigen
RCurl
regioneR
remotes
reshape
reshape2
rgl
Rgraphviz
rJava
rlang
Rmpi
rms
robustbase
ROC
rpart
rprojroot
rrcov
Rsamtools
RSQLite
rstudioapi
rtracklayer
S4Vectors
samr
sandwich
scales
scatterplot3d
segmented
sendmailR
seqinr
sessioninfo
shiny
ShortRead
simpleaffy
snow
sourcetools
sp
spam
SparseM
spatial
speedglm
splines
sqldf
stats
stats4
stringi
stringr
SummarizedExperiment
survival
sys
TCC
tcltk
tibble
tools
usethis
utf8
utils
VennDiagram
viridisLite
vsn
WGCNA
whisker
withr
XML
xopen
xtable
XVector
yaml
zlibbioc
zoo

Ruby modules

abstract
actionmailer
actionpack
actionview
activejob
activemodel
activerecord
activerecord-deprecated_finders
activesupport
addressable
arel
atk
atomic
bigdecimal
bio
buftok
builder
bundler
cairo
cmath
concurrent-ruby
crass
csv
curses
date
dbm
did_you_mean
equalizer
erubis
etc
faraday
fcgi
fcntl
fiddle
fileutils
gdbm
gdk_pixbuf2
glib2
globalid
gnuplot
gtk2
hike
hpricot
http
http_parser.rb
i18n
influxdb
io-console
ipaddr
json
loofah
mail
memoizable
metaclass
mime-types
mini_mime
mini_portile
mini_portile2
minitest
mocha
multi_json
multipart-post
mysql
naught
net-ldap
net-telnet
nokogiri
openssl
pango
passenger
pg
pkg-config
polyglot
power_assert
psych
rack
rack-test
rails
rails-deprecated_sanitizer
rails-dom-testing
rails-html-sanitizer
railties
rake
rdoc
ruby-ole
scanf
sdbm
simple_oauth
sources
spreadsheet
sprockets
sprockets-rails
stringio
strscan
test-unit
thor
thread_safe
tilt
tmail
treetop
twitter
tzinfo
webrick
xmlparser
xmlrpc
zlib

Python modules

alabaster
atomicwrites
attrs
Babel
backcall
backports.ssl-match-hostname
bamtofastq
bcbio-gff
biopython
bleach
brewer2mpl
certifi
chardet
clint2
configobj
cycler
Cython
decorator
defusedxml
DendroPy
docutils
EEL
egenix-mx-base
entrypoints
enum34
futures
h5py
HTSeq
idna
imagesize
intervaltree
ipykernel
ipython
ipython-genutils
ipywidgets
jedi
Jinja2
jsonschema
jupyter-client
jupyter-core
kiwisolver
leveldb
MACS
MACS2
MarkupSafe
matplotlib
mdtraj
mercurial
mistune
mock
more-itertools
MuPeXI
MySQL-python
natsort
nbconvert
nbformat
nglview
nose
notebook
numexpr
numpy
NumPy
packaging
pandas
pandocfilters
parse
parso
pexpect
pickleshare
Pillow
pip
pluggy
prometheus-client
prompt-toolkit
ptyprocess
py
pybedtools
PyClone
PyDP
pygist
Pygments
pygraphviz
pyparsing
pysam
pysql
pysqlite
pytest
python-dateutil
python-memcached
pytz
PyVCF
PyYAML
pyzmq
reportlab
requests
rpy2
scikit-learn
scipy
SCons
scripttest
seaborn
Send2Trash
setuptools
Seurat
shove
simplegeneric
singledispatch
six
snowballstemmer
sortedcontainers
Sphinx
sphinxcontrib-websupport
SQLAlchemy
statistics
stuf
tables
termcolor
terminado
testpath
Theano
tigmint
tornado
traitlets
umap-learn
urllib3
wcwidth
webencodings
widgetsnbextension

Perl module

Ace
AI::FANN
AI::Genetic
Algorithm::Cluster
Algorithm::Combinatorics
Algorithm::Diff
Algorithm::Diff::XS
Algorithm::Loops
Algorithm::Munkres
Algorithm::SVM
aliased
Any::Moose
App::CLI
App::gh
AppConfig
Archive::Any::Lite
Archive::Tar
Archive::Zip
Array::Compare
Array::Diff
Array::Utils
Astro::FITS::Header
Authen::NTLM
Authen::SASL
B::Hooks::EndOfScope
B::Hooks::OP::Check
bareword::filehandles
Bio
Bio::ASN1::EntrezGene
Bio::Das
Bio::DB::BioDB
Bio::DB::Das::BioSQL
Bio::DB::Das::Chado
Bio::DB::Sam
Bio::Ext::Align
Bio::Graphics
Bio::Phylo
Bio::SamTools
Bio::SCF
Bit::Vector
BSD::Resource
Business::ISBN
Business::ISBN::Data
Cache::Cache
Cache::LRU
Cache::Memcached
Calendar::Japanese::Holiday
Calendar::Simple
Canary::Stability
Capture::Tiny
Carp::Clan
CGI
CGI::Ajax
CGI::FastTemplate
CGI::Session
CGI::Simple
Chatbot
Class::Accessor
Class::Accessor::Chained
Class::Accessor::Grouped
Class::AutoClass
Class::Base
Class::Data::Inheritable
Class::DBI
Class::DBI::AbstractSearch
Class::DBI::Loader
Class::DBI::mysql
Class::DBI::Sweet
Class::Inspector
Class::ISA
Class::Load
Class::Method::Modifiers
Class::Singleton
Class::Std
Class::Std::Utils
Class::Tiny
Class::Trigger
Class::XSAccessor
Clone
common::sense
Compress::Raw::Bzip2
Compress::Raw::Zlib
Config::General
Config::IniFiles
Config::Pit
Config::Simple
Convert::ASN1
Convert::Binary::C
Convert::BinHex
Convert::EBCDIC
Convert::UU
CPAN
CPAN::DistnameInfo
CPAN::Meta
CPAN::Meta::Check
CPAN::Meta::YAML
Cpanel::JSON::XS
CPANPLUS
Crypt::DH
Crypt::DH::GMP
Crypt::OpenSSL::Random
Crypt::OpenSSL::RSA
Crypt::OpenSSL::X509
Crypt::RC4
Crypt::SSLeay
Cwd
Data
Data::Dump
Data::Dumper
Data::OptList
Data::Page
Data::Perl
Data::Section
Data::TemporaryBag
Data::UUID
Date::Calc
Date::Manip
Date::Parse
DateTime
DateTime::Format::Epoch
DateTime::Format::Mail
DateTime::Format::W3CDTF
DateTime::Locale
DateTime::TimeZone
DB_File
DB_File::Lock
DBD::Multiplex
DBD::mysql
DBD::Pg
DBD::SQLite
DBI
DBI::Shell
DBIx::Connector
DBIx::ContextualFetch
Devel::Caller
Devel::CheckCompiler
Devel::CheckLib
Devel::CoreStack
Devel::Cycle
Devel::GlobalDestruction
Devel::Hide
Devel::LexAlias
Devel::OverloadInfo
Devel::Size
Devel::StackTrace
Devel::Symdump
diffReps
Digest::HMAC
Digest::Perl::MD5
Digest::SHA
Digest::SHA1
DIME::Tools
Dist::CheckConflicts
Email::Date::Format
Encode
Encode::Locale
Error
Eval::Closure
Exception::Class
Exporter::Declare
Exporter::Tiny
ExtUtils::CBuilder
ExtUtils::Config
ExtUtils::Depends
ExtUtils::F77
ExtUtils::Helpers
ExtUtils::InstallPaths
ExtUtils::MakeMaker
ExtUtils::MakeMaker::CPANfile
ExtUtils::ParseXS
ExtUtils::PkgConfig
FCGI
Fennec::Lite
File::Copy::Recursive
File::Find::Object
File::Find::Rule
File::Grep
File::HomeDir
File::Listing
File::NFSLock
File::pushd
File::ShareDir
File::ShareDir::Install
File::Slurp
File::Slurp::Tiny
File::Slurper
File::Temp
File::Which
Font::AFM
Font::TTF
FreezeThaw
GBrowse
GD
GD::Barcode
GD::Graph
GD::Graph::histogram
GD::SVG
GD::Text
Geo::Distance
Getopt::Long::Descriptive
Getopt::Simple
Git
Graph
Graph::ReadWrite
GraphViz
Hash::AutoHash
Hash::AutoHash::Args
Hash::FieldHash
Hash::Merge
Hash::NoRef
Heap
HTML::Form
HTML::Formatter
HTML::Parser
HTML::Strip
HTML::Tagset
HTML::Template
HTML::Template::Pro
HTML::Tree
HTML-TableExtract
HTTP::Cookies
HTTP::Daemon
HTTP::Daemon::SSL
HTTP::Date
HTTP::Message
HTTP::Negotiate
HTTP::Server::Simple
Ima::DBI
Image::Magick
Image::Size
Importer
indirect
Inline
IO::Capture
IO::CaptureOutput
IO::Compress
IO::HTML
IO::Prompt
IO::SessionData
IO::Socket::SSL
IO::String
IO::Stringy
IO::Tee
IO::Tty
IPC::Run
IPC::Run3
IPC::Shareable
IRI
Jcode
JSON
JSON::Any
JSON::MaybeXS
JSON::PP
JSON::XS
Lexical::SealRequireHints
libwww::perl
libxml-perl
Lingua::EN::Inflect
Lingua::EN::Inflect::Number
List::MoreUtils
List::MoreUtils::XS
List::Util
Log::Log4perl
Log::Report
Log::Report::Optional
lsid::perl
LWP
LWP::MediaTypes
LWP::Parallel
LWP::Protocol::http10
LWP::Protocol::https
Mail
Mail::Sendmail
MailTools
Math::Bezier
Math::CDF
Math::Derivative
Math::Random
Math::Random::MT
Math::Round
Math::Spline
Math::Utils
Math::VecStat
Meta::Builder
MIME::Charset
MIME::Lite
MIME::tools
MIME::Tools
MIME::Types
MIME-tools
MLDBM
MOBY
Mock::Quick
mod_perl2
Module::Build
Module::Build::Tiny
Module::Build::XSUtil
Module::CPANfile
Module::CPANTS::Analyse
Module::ExtractUse
Module::Implementation
Module::Pluggable
Module::Refresh
Module::Runtime
Module::Runtime::Conflicts
Moo
Moose
MooX::HandlesVia
MooX::Types::MooseLike
Mouse
Mozilla::CA
MRO::Compat
multidimensional
namespace::autoclean
namespace::clean
Net
Net::DNS
Net::Google::AuthSub
Net::Google::DataAPI
Net::Google::Spreadsheets
Net::HTTP
Net::IP
Net::Jabber
Net::LDAP
Net::NTP
Net::OAuth
Net::OAuth2
Net::OpenID::Common
Net::OpenID::Consumer
Net::SMTP::SSL
Net::SSLeay
Net::Telnet
Net::Traceroute
Net::XMPP
Number::Compare
Number::Format
OLE::Storage_Lite
OpenGL
Package::DeprecationManager
Package::Stash
Package::Stash::XS
PadWalker
Params::Classify
Params::Util
Params::Validate
Params::ValidationCompiler
Parse::CPAN::Meta
Parse::RecDescent
Parse::Yapp
Path::Class
Path::Tiny
PDF::API2
PDL
Perl
Perl::Tidy
perlindex
PerlIO::gzip
PerlIO::utf8_strict
Pod::Coverage
Pod::Plainer
Pod::Spell
Pod::Spell::CommonMistakes
Pod::Strip
PostScript::Metrics
Probe::Perl
Proc::ProcessTable
RDF::Core
Readonly
Ref::Util
Ref::Util::XS
Regexp::Common
Regexp::Util
Role::Tiny
RPC::XML
Safe::Hole
Safe::World
Scope::Guard
Seeder
Set::IntSpan
Set::Scalar
SGMLSpm
SOAP::Lite
SOAP::Transport::FTP
SOAP::Transport::JABBER
SOAP::Transport::TCP
Socket
Software::License
Software::License::CCpack
Sort::Naturally
Specio
Spiffy
Spreadsheet::ParseExcel
Spreadsheet::WriteExcel
Spreadsheet::XLSX
SQL::Abstract
SQL::Abstract::Limit
Statistics::Basic
Statistics::Descriptive
Statistics::Distributions
Statistics::RankCorrelation
Statistics::TTest
Storable
strictures
String::CRC32
String::Print
Sub::Exporter
Sub::Exporter::Progressive
Sub::Identify
Sub::Info
Sub::Install
Sub::Name
Sub::Quote
Sub::Uplevel
SUPER
SVG
SVG::Graph
SWF::File
Switch
Sys::Hostname::Long
TAP::Parser::SourceHandler::pgTAP
Task::Weaken
Template
Template::Plugin::Number::Format
Template::Toolkit::Simple
Template-Plugin-Autoformat
Term::ReadKey
Term::ReadLine
Term::ReadLine::Gnu
Term::Size::Any
Term::Size::Perl
Term::Table
Test::Base
Test::CheckDeps
Test::CleanNamespaces
Test::Deep
Test::Differences
Test::Exception
Test::Exception::LessClever
Test::FailWarnings
Test::Fatal
Test::File
Test::File::ShareDir
Test::Fork
Test::Harness
Test::Harness::Straps
Test::Inter
Test::JSON
Test::Kwalitee
Test::LeakTrace
Test::Manifest
Test::Memory::Cycle
Test::MockModule
Test::MockObject
Test::MockRandom
Test::More::UTF8
Test::Most
Test::Needs
Test::NoWarnings
Test::Number::Delta
Test::Output
Test::Pod
Test::Pod::Content
Test::Pod::Coverage
Test::Regexp
Test::Requires
Test::RequiresInternet
Test::Script
Test::Simple
Test::Taint
Test::Tester
Test::use::ok
Test::UseAllModules
Test::utf8
Test::Warn
Test::Warnings
Test::Without::Module
Test::XML
Test::YAML
Test2::Plugin::NoWarnings
Test2::Suite
Text::Aligner
Text::Autoformat
Text::CSV
Text::CSV_XS
Text::Diff
Text::Format
Text::Glob
Text::Iconv
Text::Reform
Text::Scan
Text::Shellwords
Text::Table
Text::Template
Tie::DB_FileLock
Tie::DB_Lock
Tie::Hash::MultiValue
Tie::IxHash
Tie::ToObject
Tie::Watch
Time::Piece::MySQL
TimeDate
Tk
Tk::HistEntry
Tk::Pod
Tree::DAG_Node
Try::Tiny
Type::Tie
Type::Tiny
Type::Tiny::XS
Types::Serialiser
Unicode::LineBreak
Unicode::Map
Unicode::String
Unicode::UTF8
UNIVERSAL::can
UNIVERSAL::isa
UNIVERSAL::moniker
UNIVERSAL::require
URI
Variable::Magic
version
Want
WSRF::Lite
WWW::Mechanize
WWW::RobotRules
XML::Atom
XML::CanonicalizeXML
XML::CommonNS
XML::Compile
XML::Compile::Cache
XML::Compile::SOAP
XML::Compile::Tester
XML::Compile::WSDL11
XML::DOM
XML::DOM::XPath
XML::Filter::BufferText
XML::Handler::YAWriter
XML::LibXML
XML::LibXML::Simple
XML::LibXSLT
XML::Namespace
XML::NamespaceFactory
XML::NamespaceSupport
XML::Node
XML::Parser
XML::Parser::Lite
XML::Quote
XML::RegExp
XML::RSS
XML::SAX
XML::SAX::Base
XML::SAX::Expat
XML::SAX::Writer
XML::SemanticCompare
XML::SemanticDiff
XML::Simple
XML::Stream
XML::Twig
XML::Writer
XML::XPath
XML::XPathEngine
XML-DOM
YAML
YAML::LibYAML
YAML::Syck
YAML::Tiny

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Software that has been successfully used on SHIROKANE

General Freeware

Bio Freeware

R modules

Ruby modules

Python modules

Perl module

Language

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