{"id":2055,"date":"2021-04-21T04:06:19","date_gmt":"2021-04-20T19:06:19","guid":{"rendered":"https:\/\/gc.hgc.jp\/?page_id=2055"},"modified":"2021-04-21T04:06:19","modified_gmt":"2021-04-20T19:06:19","slug":"software-that-has-been-successfully-used","status":"publish","type":"page","link":"https:\/\/gc.hgc.jp\/en\/lead\/software-that-has-been-successfully-used\/","title":{"rendered":"Software that has been successfully used on SHIROKANE"},"content":{"rendered":"\n<h2>General Freeware<\/h2>\n\n\n<div data-post-id='2031' class='insert-page insert-page-2031 '>\n<ol><li>a2ps<\/li><li>AGREP<\/li><li>AMBER<\/li><li>Anaconda<\/li><li>Ant<\/li><li>APR<\/li><li>APR-util<\/li><li>ATK<\/li><li>ATLAS<\/li><li>AT-SPI2<\/li><li>Autoconf<\/li><li>AutoGen<\/li><li>Automake<\/li><li>BerkeleyDB<\/li><li>Binutils<\/li><li>Bison<\/li><li>BLAS<\/li><li>Boost<\/li><li>bzip2<\/li><li>Cairo<\/li><li>Cairomm<\/li><li>c-blosc<\/li><li>ccache<\/li><li>cdb<\/li><li>CLISP<\/li><li>CLooG<\/li><li>CMake<\/li><li>cURL<\/li><li>CVS<\/li><li>DBus<\/li><li>DBus-GLib<\/li><li>DDD<\/li><li>DejaGnu<\/li><li>Diffutils<\/li><li>DocBook-utils<\/li><li>Doxygen<\/li><li>Eclipse<\/li><li>Eigen<\/li><li>Emacs<\/li><li>Expat<\/li><li>Expect<\/li><li>FANN<\/li><li>FFmpeg<\/li><li>FFTW<\/li><li>fileutils<\/li><li>findutils<\/li><li>Flex<\/li><li>fmirror<\/li><li>Fontconfig<\/li><li>FreeType<\/li><li>FreeWnn<\/li><li>GCC<\/li><li>GConf<\/li><li>GDB<\/li><li>GDK-PixBuf<\/li><li>gettext<\/li><li>GHC<\/li><li>Ghostscript<\/li><li>Git<\/li><li>GLib<\/li><li>GLibmm<\/li><li>Glimpse<\/li><li>GlobusToolkit<\/li><li>GLPK<\/li><li>GMP<\/li><li>GnuPG<\/li><li>Gnuplot<\/li><li>google-sparsehash<\/li><li>gperf<\/li><li>GraphicsMagick<\/li><li>Graphviz<\/li><li>grep<\/li><li>GROMACS<\/li><li>GSL<\/li><li>GTK+<\/li><li>Guile<\/li><li>HarfBuzz<\/li><li>HDF5<\/li><li>HPN-SSH<\/li><li>HSCP<\/li><li>igraph<\/li><li>ImageJ<\/li><li>ImageMagick<\/li><li>Inkscape<\/li><li>isl<\/li><li>Ispell<\/li><li>Java<\/li><li>Julia<\/li><li>LAM<\/li><li>LAPACK<\/li><li>LAPACK++<\/li><li>LaTeX<\/li><li>LFTP<\/li><li>libbonobo<\/li><li>libbzip2<\/li><li>libcanberra<\/li><li>libevent<\/li><li>libffi<\/li><li>libgsf<\/li><li>libiconv<\/li><li>libIDL<\/li><li>libjpeg<\/li><li>libogg<\/li><li>libpng<\/li><li>LibreOffice<\/li><li>librsync<\/li><li>libsigc++<\/li><li>libsodium<\/li><li>libstatgrab<\/li><li>libtiff<\/li><li>Libtool<\/li><li>libungif<\/li><li>libunistring<\/li><li>libvorbis<\/li><li>libxml2<\/li><li>libXpm<\/li><li>libyaml<\/li><li>LittleCMS<\/li><li>Lua<\/li><li>LV<\/li><li>Lynx<\/li><li>LZ4<\/li><li>M4<\/li><li>Make<\/li><li>MATLAB_Compiler_Runtime<\/li><li>matrix-toolkits-java<\/li><li>Mercurial<\/li><li>Mew<\/li><li>mgzip<\/li><li>MH<\/li><li>MolScript<\/li><li>MongoDB<\/li><li>MPC<\/li><li>MPFR<\/li><li>MPICH<\/li><li>MPICH2<\/li><li>mpiJava<\/li><li>MySQL<\/li><li>NcFTP<\/li><li>ncurses<\/li><li>NetCDF<\/li><li>netlib-java<\/li><li>nkf<\/li><li>Node.js<\/li><li>Octave<\/li><li>OpenBabel<\/li><li>OpenCV<\/li><li>OpenJPEG<\/li><li>OpenMotif<\/li><li>OpenMPI<\/li><li>OpenSlide<\/li><li>OpenSSL<\/li><li>ORBit2<\/li><li>P7ZIP<\/li><li>Pango<\/li><li>Pangomm<\/li><li>Parallel<\/li><li>PBZIP2<\/li><li>PCRE<\/li><li>pdsh<\/li><li>Perl<\/li><li>PHP<\/li><li>Pixman<\/li><li>pkg-config<\/li><li>plotutils<\/li><li>POPT<\/li><li>PostgreSQL<\/li><li>POV-Ray<\/li><li>PPL<\/li><li>Python<\/li><li>Qt<\/li><li>R<\/li><li>Readline<\/li><li>RLPR<\/li><li>RStudio<\/li><li>RStudio Desktop<\/li><li>rsync<\/li><li>Ruby<\/li><li>SBCL<\/li><li>screen<\/li><li>Serf<\/li><li>Singularity<\/li><li>SoX<\/li><li>SQLite<\/li><li>STLport<\/li><li>Subversion<\/li><li>SUNDIALS<\/li><li>SVN<\/li><li>SWIG<\/li><li>tar<\/li><li>Tcl<\/li><li>teTex<\/li><li>Texinfo<\/li><li>Tk<\/li><li>tmux<\/li><li>tree<\/li><li>VIPS<\/li><li>wget<\/li><li>Xerces-C++<\/li><li>XQilla<\/li><li>XZ_Utils<\/li><li>Yasm<\/li><li>ZeroMQ<\/li><li>zlib<\/li><\/ol>\n<\/div>\n\n\n\n<h2>Bio Freeware<\/h2>\n\n\n<div data-post-id='2032' class='insert-page insert-page-2032 '>\n<ol><li>ABySS<\/li><li>ALSCRIPT<\/li><li>AmberTools<\/li><li>APT<\/li><li>ARCS<\/li><li>AUGUSTUS<\/li><li>BamTools<\/li><li>bcl2fastq<\/li><li>BCL2FASTQ<\/li><li>BEAGLE<\/li><li>BEAST<\/li><li>BEDTools<\/li><li>biobambam2<\/li><li>Bioconductor<\/li><li>Biopieces<\/li><li>Bioscope<\/li><li>BLAST<\/li><li>BLAST+<\/li><li>BLAT<\/li><li>Bowtie<\/li><li>Bowtie2<\/li><li>BWA<\/li><li>Canu<\/li><li>CAP3<\/li><li>CD-HIT<\/li><li>Circos<\/li><li>ClustalW<\/li><li>COPASI<\/li><li>CREAD<\/li><li>Cufflinks<\/li><li>Cytoscape<\/li><li>Darn<\/li><li>DIAMOND<\/li><li>DROMPA<\/li><li>EMBOSS<\/li><li>Exonerate<\/li><li>eXpress<\/li><li>FALCON<\/li><li>FasnQC<\/li><li>FasnTree<\/li><li>FASTA<\/li><li>FastML<\/li><li>FastQC<\/li><li>FastTree<\/li><li>FASTX-Toolkit<\/li><li>FreeBayes<\/li><li>GENESIS<\/li><li>GeneTorrent<\/li><li>GMAP<\/li><li>HISAT<\/li><li>HISAT2<\/li><li>HMMER<\/li><li>IgBLAST<\/li><li>IGV<\/li><li>InterProScan<\/li><li>io_lib<\/li><li>Ion-Variant-Hunter<\/li><li>Jellyfish<\/li><li>JGAP<\/li><li>Juicer<\/li><li>Karn<\/li><li>kClust<\/li><li>libGTextUtils<\/li><li>libsequence<\/li><li>lobSTR<\/li><li>MAFFT<\/li><li>Maq<\/li><li>MATLAB<\/li><li>MCL<\/li><li>MEGAHIT<\/li><li>MEME<\/li><li>MEME Suite<\/li><li>Meta-MEME<\/li><li>Minimap<\/li><li>MMseqs<\/li><li>MolScript<\/li><li>MUMmer<\/li><li>NCBI_Toolkit<\/li><li>NCBI-CXX-Toolkin<\/li><li>NEURON<\/li><li>NovoAlign<\/li><li>ORFfinder<\/li><li>PASA<\/li><li>PGENESIS<\/li><li>PHYLIP<\/li><li>phyx<\/li><li>Picard<\/li><li>Platanus<\/li><li>Polysolver<\/li><li>PRANK<\/li><li>Prodigal<\/li><li>RasMol<\/li><li>Raster3D<\/li><li>RAxML<\/li><li>Roary<\/li><li>Salmon<\/li><li>SAMtools<\/li><li>SEER<\/li><li>SICER<\/li><li>SnpEff<\/li><li>SnringTie<\/li><li>SOAPdenovo<\/li><li>SOAPdenovo2<\/li><li>SPAdes<\/li><li>SRA<\/li><li>SRA-Toolkin<\/li><li>SSAKE<\/li><li>STAR<\/li><li>StochKit<\/li><li>StringTie<\/li><li>Tandem_Repeats_Finder<\/li><li>TMAP<\/li><li>TopHat<\/li><li>Torrent_Variant_Caller<\/li><li>TorrentSuite<\/li><li>TRF<\/li><li>Trinity<\/li><li>VariationHunter<\/li><li>VCFtools<\/li><li>Velven<\/li><li>Velvet<\/li><li>VelvetOptimiser<\/li><li>vidjil-algo<\/li><li>VMD<\/li><li>VSEARCH<\/li><\/ol>\n<\/div>\n\n\n\n<h2>R modules<\/h2>\n\n\n<div data-post-id='2041' class='insert-page insert-page-2041 '>\n<ol><li>abind<\/li><li>acepack<\/li><li>ade4<\/li><li>affy<\/li><li>affydata<\/li><li>affyio<\/li><li>affyPLM<\/li><li>affyQCReport<\/li><li>akima<\/li><li>annaffy<\/li><li>annotate<\/li><li>AnnotationDbi<\/li><li>AnnotationForge<\/li><li>AnnotationHub<\/li><li>ape<\/li><li>askpass<\/li><li>assertthat<\/li><li>ath1121501cdf<\/li><li>ath1121501probe<\/li><li>backports<\/li><li>base<\/li><li>base64enc<\/li><li>BatchJobs<\/li><li>baySeq<\/li><li>BBmisc<\/li><li>beanplot<\/li><li>BH<\/li><li>BiasedUrn<\/li><li>Biobase<\/li><li>BiocGenerics<\/li><li>BiocInstaller<\/li><li>BiocParallel<\/li><li>biomaRt<\/li><li>Biostrings<\/li><li>bitops<\/li><li>BMA<\/li><li>boot<\/li><li>brew<\/li><li>BSgenome<\/li><li>callr<\/li><li>Category<\/li><li>caTools<\/li><li>checkmate<\/li><li>ChIPpeakAnno<\/li><li>chron<\/li><li>class<\/li><li>cli<\/li><li>clipr<\/li><li>clisymbols<\/li><li>cluster<\/li><li>codetools<\/li><li>coloc<\/li><li>colorspace<\/li><li>compiler<\/li><li>crayon<\/li><li>curl<\/li><li>datasets<\/li><li>DBI<\/li><li>DEoptimR<\/li><li>desc<\/li><li>DESeq<\/li><li>DESeq2<\/li><li>devtools<\/li><li>dichromat<\/li><li>digest<\/li><li>dplyr<\/li><li>DPpackage<\/li><li>dynamicTreeCut<\/li><li>DynDoc<\/li><li>edgeR<\/li><li>ensembldb<\/li><li>evaluate<\/li><li>fail<\/li><li>fansi<\/li><li>fields<\/li><li>flashClust<\/li><li>foreach<\/li><li>foreign<\/li><li>formatR<\/li><li>Formula<\/li><li>fpc<\/li><li>fs<\/li><li>gcrma<\/li><li>gdata<\/li><li>gee<\/li><li>genefilter<\/li><li>geneLenDataBase<\/li><li>geneplotter<\/li><li>GenomeInfoDb<\/li><li>GenomicAlignments<\/li><li>GenomicFeatures<\/li><li>GenomicRanges<\/li><li>ggplot2<\/li><li>gh<\/li><li>git2r<\/li><li>glmmML<\/li><li>glue<\/li><li>gmodels<\/li><li>goseq<\/li><li>GOstats<\/li><li>gplots<\/li><li>graph<\/li><li>graphics<\/li><li>grDevices<\/li><li>grid<\/li><li>gridExtra<\/li><li>GSEABase<\/li><li>gsubfn<\/li><li>gtable<\/li><li>gtools<\/li><li>hexbin<\/li><li>hgu133plus2cdf<\/li><li>hiAnnotator<\/li><li>highr<\/li><li>Hmisc<\/li><li>htmltools<\/li><li>htmlwidgets<\/li><li>httpuv<\/li><li>httr<\/li><li>hwriter<\/li><li>idr<\/li><li>impute<\/li><li>ini<\/li><li>inline<\/li><li>IRanges<\/li><li>iterators<\/li><li>itertools<\/li><li>jsonlite<\/li><li>KernSmooth<\/li><li>knitr<\/li><li>labeling<\/li><li>lattice<\/li><li>latticeExtra<\/li><li>lazy<\/li><li>lazyeval<\/li><li>leaps<\/li><li>limma<\/li><li>lme4<\/li><li>locfit<\/li><li>magrittr<\/li><li>maps<\/li><li>markdown<\/li><li>marray<\/li><li>MASS<\/li><li>Matrix<\/li><li>MatrixModels<\/li><li>matrixStats<\/li><li>mclust<\/li><li>memoise<\/li><li>methods<\/li><li>mgcv<\/li><li>mime<\/li><li>minqa<\/li><li>mouse4302cdf<\/li><li>multcomp<\/li><li>multtest<\/li><li>munsell<\/li><li>mvtnorm<\/li><li>nlme<\/li><li>nloptr<\/li><li>nnet<\/li><li>openssl<\/li><li>parallel<\/li><li>pcaPP<\/li><li>PEER<\/li><li>perm<\/li><li>pillar<\/li><li>pkgbuild<\/li><li>pkgconfig<\/li><li>pkgload<\/li><li>plyr<\/li><li>polspline<\/li><li>preprocessCore<\/li><li>prettyunits<\/li><li>processx<\/li><li>proto<\/li><li>ps<\/li><li>purrr<\/li><li>quantreg<\/li><li>R6<\/li><li>rae230acdf<\/li><li>rat2302cdf<\/li><li>RBGL<\/li><li>rcmdcheck<\/li><li>RColorBrewer<\/li><li>Rcpp<\/li><li>RcppArmadillo<\/li><li>RcppEigen<\/li><li>RCurl<\/li><li>regioneR<\/li><li>remotes<\/li><li>reshape<\/li><li>reshape2<\/li><li>rgl<\/li><li>Rgraphviz<\/li><li>rJava<\/li><li>rlang<\/li><li>Rmpi<\/li><li>rms<\/li><li>robustbase<\/li><li>ROC<\/li><li>rpart<\/li><li>rprojroot<\/li><li>rrcov<\/li><li>Rsamtools<\/li><li>RSQLite<\/li><li>rstudioapi<\/li><li>rtracklayer<\/li><li>S4Vectors<\/li><li>samr<\/li><li>sandwich<\/li><li>scales<\/li><li>scatterplot3d<\/li><li>segmented<\/li><li>sendmailR<\/li><li>seqinr<\/li><li>sessioninfo<\/li><li>shiny<\/li><li>ShortRead<\/li><li>simpleaffy<\/li><li>snow<\/li><li>sourcetools<\/li><li>sp<\/li><li>spam<\/li><li>SparseM<\/li><li>spatial<\/li><li>speedglm<\/li><li>splines<\/li><li>sqldf<\/li><li>stats<\/li><li>stats4<\/li><li>stringi<\/li><li>stringr<\/li><li>SummarizedExperiment<\/li><li>survival<\/li><li>sys<\/li><li>TCC<\/li><li>tcltk<\/li><li>tibble<\/li><li>tools<\/li><li>usethis<\/li><li>utf8<\/li><li>utils<\/li><li>VennDiagram<\/li><li>viridisLite<\/li><li>vsn<\/li><li>WGCNA<\/li><li>whisker<\/li><li>withr<\/li><li>XML<\/li><li>xopen<\/li><li>xtable<\/li><li>XVector<\/li><li>yaml<\/li><li>zlibbioc<\/li><li>zoo<\/li><\/ol>\n<\/div>\n\n\n\n<h2>Ruby modules<\/h2>\n\n\n<div data-post-id='2045' class='insert-page insert-page-2045 '>\n<ol><li>abstract<\/li><li>actionmailer<\/li><li>actionpack<\/li><li>actionview<\/li><li>activejob<\/li><li>activemodel<\/li><li>activerecord<\/li><li>activerecord-deprecated_finders<\/li><li>activesupport<\/li><li>addressable<\/li><li>arel<\/li><li>atk<\/li><li>atomic<\/li><li>bigdecimal<\/li><li>bio<\/li><li>buftok<\/li><li>builder<\/li><li>bundler<\/li><li>cairo<\/li><li>cmath<\/li><li>concurrent-ruby<\/li><li>crass<\/li><li>csv<\/li><li>curses<\/li><li>date<\/li><li>dbm<\/li><li>did_you_mean<\/li><li>equalizer<\/li><li>erubis<\/li><li>etc<\/li><li>faraday<\/li><li>fcgi<\/li><li>fcntl<\/li><li>fiddle<\/li><li>fileutils<\/li><li>gdbm<\/li><li>gdk_pixbuf2<\/li><li>glib2<\/li><li>globalid<\/li><li>gnuplot<\/li><li>gtk2<\/li><li>hike<\/li><li>hpricot<\/li><li>http<\/li><li>http_parser.rb<\/li><li>i18n<\/li><li>influxdb<\/li><li>io-console<\/li><li>ipaddr<\/li><li>json<\/li><li>loofah<\/li><li>mail<\/li><li>memoizable<\/li><li>metaclass<\/li><li>mime-types<\/li><li>mini_mime<\/li><li>mini_portile<\/li><li>mini_portile2<\/li><li>minitest<\/li><li>mocha<\/li><li>multi_json<\/li><li>multipart-post<\/li><li>mysql<\/li><li>naught<\/li><li>net-ldap<\/li><li>net-telnet<\/li><li>nokogiri<\/li><li>openssl<\/li><li>pango<\/li><li>passenger<\/li><li>pg<\/li><li>pkg-config<\/li><li>polyglot<\/li><li>power_assert<\/li><li>psych<\/li><li>rack<\/li><li>rack-test<\/li><li>rails<\/li><li>rails-deprecated_sanitizer<\/li><li>rails-dom-testing<\/li><li>rails-html-sanitizer<\/li><li>railties<\/li><li>rake<\/li><li>rdoc<\/li><li>ruby-ole<\/li><li>scanf<\/li><li>sdbm<\/li><li>simple_oauth<\/li><li>sources<\/li><li>spreadsheet<\/li><li>sprockets<\/li><li>sprockets-rails<\/li><li>stringio<\/li><li>strscan<\/li><li>test-unit<\/li><li>thor<\/li><li>thread_safe<\/li><li>tilt<\/li><li>tmail<\/li><li>treetop<\/li><li>twitter<\/li><li>tzinfo<\/li><li>webrick<\/li><li>xmlparser<\/li><li>xmlrpc<\/li><li>zlib<\/li><\/ol>\n<\/div>\n\n\n\n<h2>Python modules <\/h2>\n\n\n<div data-post-id='2048' class='insert-page insert-page-2048 '>\n<ol><li>alabaster<\/li><li>atomicwrites<\/li><li>attrs<\/li><li>Babel<\/li><li>backcall<\/li><li>backports.ssl-match-hostname<\/li><li>bamtofastq<\/li><li>bcbio-gff<\/li><li>biopython<\/li><li>bleach<\/li><li>brewer2mpl<\/li><li>certifi<\/li><li>chardet<\/li><li>clint2<\/li><li>configobj<\/li><li>cycler<\/li><li>Cython<\/li><li>decorator<\/li><li>defusedxml<\/li><li>DendroPy<\/li><li>docutils<\/li><li>EEL<\/li><li>egenix-mx-base<\/li><li>entrypoints<\/li><li>enum34<\/li><li>futures<\/li><li>h5py<\/li><li>HTSeq<\/li><li>idna<\/li><li>imagesize<\/li><li>intervaltree<\/li><li>ipykernel<\/li><li>ipython<\/li><li>ipython-genutils<\/li><li>ipywidgets<\/li><li>jedi<\/li><li>Jinja2<\/li><li>jsonschema<\/li><li>jupyter-client<\/li><li>jupyter-core<\/li><li>kiwisolver<\/li><li>leveldb<\/li><li>MACS<\/li><li>MACS2<\/li><li>MarkupSafe<\/li><li>matplotlib<\/li><li>mdtraj<\/li><li>mercurial<\/li><li>mistune<\/li><li>mock<\/li><li>more-itertools<\/li><li>MuPeXI<\/li><li>MySQL-python<\/li><li>natsort<\/li><li>nbconvert<\/li><li>nbformat<\/li><li>nglview<\/li><li>nose<\/li><li>notebook<\/li><li>numexpr<\/li><li>numpy<\/li><li>NumPy<\/li><li>packaging<\/li><li>pandas<\/li><li>pandocfilters<\/li><li>parse<\/li><li>parso<\/li><li>pexpect<\/li><li>pickleshare<\/li><li>Pillow<\/li><li>pip<\/li><li>pluggy<\/li><li>prometheus-client<\/li><li>prompt-toolkit<\/li><li>ptyprocess<\/li><li>py<\/li><li>pybedtools<\/li><li>PyClone<\/li><li>PyDP<\/li><li>pygist<\/li><li>Pygments<\/li><li>pygraphviz<\/li><li>pyparsing<\/li><li>pysam<\/li><li>pysql<\/li><li>pysqlite<\/li><li>pytest<\/li><li>python-dateutil<\/li><li>python-memcached<\/li><li>pytz<\/li><li>PyVCF<\/li><li>PyYAML<\/li><li>pyzmq<\/li><li>reportlab<\/li><li>requests<\/li><li>rpy2<\/li><li>scikit-learn<\/li><li>scipy<\/li><li>SCons<\/li><li>scripttest<\/li><li>seaborn<\/li><li>Send2Trash<\/li><li>setuptools<\/li><li>Seurat<\/li><li>shove<\/li><li>simplegeneric<\/li><li>singledispatch<\/li><li>six<\/li><li>snowballstemmer<\/li><li>sortedcontainers<\/li><li>Sphinx<\/li><li>sphinxcontrib-websupport<\/li><li>SQLAlchemy<\/li><li>statistics<\/li><li>stuf<\/li><li>tables<\/li><li>termcolor<\/li><li>terminado<\/li><li>testpath<\/li><li>Theano<\/li><li>tigmint<\/li><li>tornado<\/li><li>traitlets<\/li><li>umap-learn<\/li><li>urllib3<\/li><li>wcwidth<\/li><li>webencodings<\/li><li>widgetsnbextension<\/li><\/ol>\n<\/div>\n\n\n\n<h2>Perl module<\/h2>\n\n\n<div data-post-id='2051' class='insert-page insert-page-2051 '>\n<ol><li>Ace<\/li><li>AI::FANN<\/li><li>AI::Genetic<\/li><li>Algorithm::Cluster<\/li><li>Algorithm::Combinatorics<\/li><li>Algorithm::Diff<\/li><li>Algorithm::Diff::XS<\/li><li>Algorithm::Loops<\/li><li>Algorithm::Munkres<\/li><li>Algorithm::SVM<\/li><li>aliased<\/li><li>Any::Moose<\/li><li>App::CLI<\/li><li>App::gh<\/li><li>AppConfig<\/li><li>Archive::Any::Lite<\/li><li>Archive::Tar<\/li><li>Archive::Zip<\/li><li>Array::Compare<\/li><li>Array::Diff<\/li><li>Array::Utils<\/li><li>Astro::FITS::Header<\/li><li>Authen::NTLM<\/li><li>Authen::SASL<\/li><li>B::Hooks::EndOfScope<\/li><li>B::Hooks::OP::Check<\/li><li>bareword::filehandles<\/li><li>Bio<\/li><li>Bio::ASN1::EntrezGene<\/li><li>Bio::Das<\/li><li>Bio::DB::BioDB<\/li><li>Bio::DB::Das::BioSQL<\/li><li>Bio::DB::Das::Chado<\/li><li>Bio::DB::Sam<\/li><li>Bio::Ext::Align<\/li><li>Bio::Graphics<\/li><li>Bio::Phylo<\/li><li>Bio::SamTools<\/li><li>Bio::SCF<\/li><li>Bit::Vector<\/li><li>BSD::Resource<\/li><li>Business::ISBN<\/li><li>Business::ISBN::Data<\/li><li>Cache::Cache<\/li><li>Cache::LRU<\/li><li>Cache::Memcached<\/li><li>Calendar::Japanese::Holiday<\/li><li>Calendar::Simple<\/li><li>Canary::Stability<\/li><li>Capture::Tiny<\/li><li>Carp::Clan<\/li><li>CGI<\/li><li>CGI::Ajax<\/li><li>CGI::FastTemplate<\/li><li>CGI::Session<\/li><li>CGI::Simple<\/li><li>Chatbot<\/li><li>Class::Accessor<\/li><li>Class::Accessor::Chained<\/li><li>Class::Accessor::Grouped<\/li><li>Class::AutoClass<\/li><li>Class::Base<\/li><li>Class::Data::Inheritable<\/li><li>Class::DBI<\/li><li>Class::DBI::AbstractSearch<\/li><li>Class::DBI::Loader<\/li><li>Class::DBI::mysql<\/li><li>Class::DBI::Sweet<\/li><li>Class::Inspector<\/li><li>Class::ISA<\/li><li>Class::Load<\/li><li>Class::Method::Modifiers<\/li><li>Class::Singleton<\/li><li>Class::Std<\/li><li>Class::Std::Utils<\/li><li>Class::Tiny<\/li><li>Class::Trigger<\/li><li>Class::XSAccessor<\/li><li>Clone<\/li><li>common::sense<\/li><li>Compress::Raw::Bzip2<\/li><li>Compress::Raw::Zlib<\/li><li>Config::General<\/li><li>Config::IniFiles<\/li><li>Config::Pit<\/li><li>Config::Simple<\/li><li>Convert::ASN1<\/li><li>Convert::Binary::C<\/li><li>Convert::BinHex<\/li><li>Convert::EBCDIC<\/li><li>Convert::UU<\/li><li>CPAN<\/li><li>CPAN::DistnameInfo<\/li><li>CPAN::Meta<\/li><li>CPAN::Meta::Check<\/li><li>CPAN::Meta::YAML<\/li><li>Cpanel::JSON::XS<\/li><li>CPANPLUS<\/li><li>Crypt::DH<\/li><li>Crypt::DH::GMP<\/li><li>Crypt::OpenSSL::Random<\/li><li>Crypt::OpenSSL::RSA<\/li><li>Crypt::OpenSSL::X509<\/li><li>Crypt::RC4<\/li><li>Crypt::SSLeay<\/li><li>Cwd<\/li><li>Data<\/li><li>Data::Dump<\/li><li>Data::Dumper<\/li><li>Data::OptList<\/li><li>Data::Page<\/li><li>Data::Perl<\/li><li>Data::Section<\/li><li>Data::TemporaryBag<\/li><li>Data::UUID<\/li><li>Date::Calc<\/li><li>Date::Manip<\/li><li>Date::Parse<\/li><li>DateTime<\/li><li>DateTime::Format::Epoch<\/li><li>DateTime::Format::Mail<\/li><li>DateTime::Format::W3CDTF<\/li><li>DateTime::Locale<\/li><li>DateTime::TimeZone<\/li><li>DB_File<\/li><li>DB_File::Lock<\/li><li>DBD::Multiplex<\/li><li>DBD::mysql<\/li><li>DBD::Pg<\/li><li>DBD::SQLite<\/li><li>DBI<\/li><li>DBI::Shell<\/li><li>DBIx::Connector<\/li><li>DBIx::ContextualFetch<\/li><li>Devel::Caller<\/li><li>Devel::CheckCompiler<\/li><li>Devel::CheckLib<\/li><li>Devel::CoreStack<\/li><li>Devel::Cycle<\/li><li>Devel::GlobalDestruction<\/li><li>Devel::Hide<\/li><li>Devel::LexAlias<\/li><li>Devel::OverloadInfo<\/li><li>Devel::Size<\/li><li>Devel::StackTrace<\/li><li>Devel::Symdump<\/li><li>diffReps<\/li><li>Digest::HMAC<\/li><li>Digest::Perl::MD5<\/li><li>Digest::SHA<\/li><li>Digest::SHA1<\/li><li>DIME::Tools<\/li><li>Dist::CheckConflicts<\/li><li>Email::Date::Format<\/li><li>Encode<\/li><li>Encode::Locale<\/li><li>Error<\/li><li>Eval::Closure<\/li><li>Exception::Class<\/li><li>Exporter::Declare<\/li><li>Exporter::Tiny<\/li><li>ExtUtils::CBuilder<\/li><li>ExtUtils::Config<\/li><li>ExtUtils::Depends<\/li><li>ExtUtils::F77<\/li><li>ExtUtils::Helpers<\/li><li>ExtUtils::InstallPaths<\/li><li>ExtUtils::MakeMaker<\/li><li>ExtUtils::MakeMaker::CPANfile<\/li><li>ExtUtils::ParseXS<\/li><li>ExtUtils::PkgConfig<\/li><li>FCGI<\/li><li>Fennec::Lite<\/li><li>File::Copy::Recursive<\/li><li>File::Find::Object<\/li><li>File::Find::Rule<\/li><li>File::Grep<\/li><li>File::HomeDir<\/li><li>File::Listing<\/li><li>File::NFSLock<\/li><li>File::pushd<\/li><li>File::ShareDir<\/li><li>File::ShareDir::Install<\/li><li>File::Slurp<\/li><li>File::Slurp::Tiny<\/li><li>File::Slurper<\/li><li>File::Temp<\/li><li>File::Which<\/li><li>Font::AFM<\/li><li>Font::TTF<\/li><li>FreezeThaw<\/li><li>GBrowse<\/li><li>GD<\/li><li>GD::Barcode<\/li><li>GD::Graph<\/li><li>GD::Graph::histogram<\/li><li>GD::SVG<\/li><li>GD::Text<\/li><li>Geo::Distance<\/li><li>Getopt::Long::Descriptive<\/li><li>Getopt::Simple<\/li><li>Git<\/li><li>Graph<\/li><li>Graph::ReadWrite<\/li><li>GraphViz<\/li><li>Hash::AutoHash<\/li><li>Hash::AutoHash::Args<\/li><li>Hash::FieldHash<\/li><li>Hash::Merge<\/li><li>Hash::NoRef<\/li><li>Heap<\/li><li>HTML::Form<\/li><li>HTML::Formatter<\/li><li>HTML::Parser<\/li><li>HTML::Strip<\/li><li>HTML::Tagset<\/li><li>HTML::Template<\/li><li>HTML::Template::Pro<\/li><li>HTML::Tree<\/li><li>HTML-TableExtract<\/li><li>HTTP::Cookies<\/li><li>HTTP::Daemon<\/li><li>HTTP::Daemon::SSL<\/li><li>HTTP::Date<\/li><li>HTTP::Message<\/li><li>HTTP::Negotiate<\/li><li>HTTP::Server::Simple<\/li><li>Ima::DBI<\/li><li>Image::Magick<\/li><li>Image::Size<\/li><li>Importer<\/li><li>indirect<\/li><li>Inline<\/li><li>IO::Capture<\/li><li>IO::CaptureOutput<\/li><li>IO::Compress<\/li><li>IO::HTML<\/li><li>IO::Prompt<\/li><li>IO::SessionData<\/li><li>IO::Socket::SSL<\/li><li>IO::String<\/li><li>IO::Stringy<\/li><li>IO::Tee<\/li><li>IO::Tty<\/li><li>IPC::Run<\/li><li>IPC::Run3<\/li><li>IPC::Shareable<\/li><li>IRI<\/li><li>Jcode<\/li><li>JSON<\/li><li>JSON::Any<\/li><li>JSON::MaybeXS<\/li><li>JSON::PP<\/li><li>JSON::XS<\/li><li>Lexical::SealRequireHints<\/li><li>libwww::perl<\/li><li>libxml-perl<\/li><li>Lingua::EN::Inflect<\/li><li>Lingua::EN::Inflect::Number<\/li><li>List::MoreUtils<\/li><li>List::MoreUtils::XS<\/li><li>List::Util<\/li><li>Log::Log4perl<\/li><li>Log::Report<\/li><li>Log::Report::Optional<\/li><li>lsid::perl<\/li><li>LWP<\/li><li>LWP::MediaTypes<\/li><li>LWP::Parallel<\/li><li>LWP::Protocol::http10<\/li><li>LWP::Protocol::https<\/li><li>Mail<\/li><li>Mail::Sendmail<\/li><li>MailTools<\/li><li>Math::Bezier<\/li><li>Math::CDF<\/li><li>Math::Derivative<\/li><li>Math::Random<\/li><li>Math::Random::MT<\/li><li>Math::Round<\/li><li>Math::Spline<\/li><li>Math::Utils<\/li><li>Math::VecStat<\/li><li>Meta::Builder<\/li><li>MIME::Charset<\/li><li>MIME::Lite<\/li><li>MIME::tools<\/li><li>MIME::Tools<\/li><li>MIME::Types<\/li><li>MIME-tools<\/li><li>MLDBM<\/li><li>MOBY<\/li><li>Mock::Quick<\/li><li>mod_perl2<\/li><li>Module::Build<\/li><li>Module::Build::Tiny<\/li><li>Module::Build::XSUtil<\/li><li>Module::CPANfile<\/li><li>Module::CPANTS::Analyse<\/li><li>Module::ExtractUse<\/li><li>Module::Implementation<\/li><li>Module::Pluggable<\/li><li>Module::Refresh<\/li><li>Module::Runtime<\/li><li>Module::Runtime::Conflicts<\/li><li>Moo<\/li><li>Moose<\/li><li>MooX::HandlesVia<\/li><li>MooX::Types::MooseLike<\/li><li>Mouse<\/li><li>Mozilla::CA<\/li><li>MRO::Compat<\/li><li>multidimensional<\/li><li>namespace::autoclean<\/li><li>namespace::clean<\/li><li>Net<\/li><li>Net::DNS<\/li><li>Net::Google::AuthSub<\/li><li>Net::Google::DataAPI<\/li><li>Net::Google::Spreadsheets<\/li><li>Net::HTTP<\/li><li>Net::IP<\/li><li>Net::Jabber<\/li><li>Net::LDAP<\/li><li>Net::NTP<\/li><li>Net::OAuth<\/li><li>Net::OAuth2<\/li><li>Net::OpenID::Common<\/li><li>Net::OpenID::Consumer<\/li><li>Net::SMTP::SSL<\/li><li>Net::SSLeay<\/li><li>Net::Telnet<\/li><li>Net::Traceroute<\/li><li>Net::XMPP<\/li><li>Number::Compare<\/li><li>Number::Format<\/li><li>OLE::Storage_Lite<\/li><li>OpenGL<\/li><li>Package::DeprecationManager<\/li><li>Package::Stash<\/li><li>Package::Stash::XS<\/li><li>PadWalker<\/li><li>Params::Classify<\/li><li>Params::Util<\/li><li>Params::Validate<\/li><li>Params::ValidationCompiler<\/li><li>Parse::CPAN::Meta<\/li><li>Parse::RecDescent<\/li><li>Parse::Yapp<\/li><li>Path::Class<\/li><li>Path::Tiny<\/li><li>PDF::API2<\/li><li>PDL<\/li><li>Perl<\/li><li>Perl::Tidy<\/li><li>perlindex<\/li><li>PerlIO::gzip<\/li><li>PerlIO::utf8_strict<\/li><li>Pod::Coverage<\/li><li>Pod::Plainer<\/li><li>Pod::Spell<\/li><li>Pod::Spell::CommonMistakes<\/li><li>Pod::Strip<\/li><li>PostScript::Metrics<\/li><li>Probe::Perl<\/li><li>Proc::ProcessTable<\/li><li>RDF::Core<\/li><li>Readonly<\/li><li>Ref::Util<\/li><li>Ref::Util::XS<\/li><li>Regexp::Common<\/li><li>Regexp::Util<\/li><li>Role::Tiny<\/li><li>RPC::XML<\/li><li>Safe::Hole<\/li><li>Safe::World<\/li><li>Scope::Guard<\/li><li>Seeder<\/li><li>Set::IntSpan<\/li><li>Set::Scalar<\/li><li>SGMLSpm<\/li><li>SOAP::Lite<\/li><li>SOAP::Transport::FTP<\/li><li>SOAP::Transport::JABBER<\/li><li>SOAP::Transport::TCP<\/li><li>Socket<\/li><li>Software::License<\/li><li>Software::License::CCpack<\/li><li>Sort::Naturally<\/li><li>Specio<\/li><li>Spiffy<\/li><li>Spreadsheet::ParseExcel<\/li><li>Spreadsheet::WriteExcel<\/li><li>Spreadsheet::XLSX<\/li><li>SQL::Abstract<\/li><li>SQL::Abstract::Limit<\/li><li>Statistics::Basic<\/li><li>Statistics::Descriptive<\/li><li>Statistics::Distributions<\/li><li>Statistics::RankCorrelation<\/li><li>Statistics::TTest<\/li><li>Storable<\/li><li>strictures<\/li><li>String::CRC32<\/li><li>String::Print<\/li><li>Sub::Exporter<\/li><li>Sub::Exporter::Progressive<\/li><li>Sub::Identify<\/li><li>Sub::Info<\/li><li>Sub::Install<\/li><li>Sub::Name<\/li><li>Sub::Quote<\/li><li>Sub::Uplevel<\/li><li>SUPER<\/li><li>SVG<\/li><li>SVG::Graph<\/li><li>SWF::File<\/li><li>Switch<\/li><li>Sys::Hostname::Long<\/li><li>TAP::Parser::SourceHandler::pgTAP<\/li><li>Task::Weaken<\/li><li>Template<\/li><li>Template::Plugin::Number::Format<\/li><li>Template::Toolkit::Simple<\/li><li>Template-Plugin-Autoformat<\/li><li>Term::ReadKey<\/li><li>Term::ReadLine<\/li><li>Term::ReadLine::Gnu<\/li><li>Term::Size::Any<\/li><li>Term::Size::Perl<\/li><li>Term::Table<\/li><li>Test::Base<\/li><li>Test::CheckDeps<\/li><li>Test::CleanNamespaces<\/li><li>Test::Deep<\/li><li>Test::Differences<\/li><li>Test::Exception<\/li><li>Test::Exception::LessClever<\/li><li>Test::FailWarnings<\/li><li>Test::Fatal<\/li><li>Test::File<\/li><li>Test::File::ShareDir<\/li><li>Test::Fork<\/li><li>Test::Harness<\/li><li>Test::Harness::Straps<\/li><li>Test::Inter<\/li><li>Test::JSON<\/li><li>Test::Kwalitee<\/li><li>Test::LeakTrace<\/li><li>Test::Manifest<\/li><li>Test::Memory::Cycle<\/li><li>Test::MockModule<\/li><li>Test::MockObject<\/li><li>Test::MockRandom<\/li><li>Test::More::UTF8<\/li><li>Test::Most<\/li><li>Test::Needs<\/li><li>Test::NoWarnings<\/li><li>Test::Number::Delta<\/li><li>Test::Output<\/li><li>Test::Pod<\/li><li>Test::Pod::Content<\/li><li>Test::Pod::Coverage<\/li><li>Test::Regexp<\/li><li>Test::Requires<\/li><li>Test::RequiresInternet<\/li><li>Test::Script<\/li><li>Test::Simple<\/li><li>Test::Taint<\/li><li>Test::Tester<\/li><li>Test::use::ok<\/li><li>Test::UseAllModules<\/li><li>Test::utf8<\/li><li>Test::Warn<\/li><li>Test::Warnings<\/li><li>Test::Without::Module<\/li><li>Test::XML<\/li><li>Test::YAML<\/li><li>Test2::Plugin::NoWarnings<\/li><li>Test2::Suite<\/li><li>Text::Aligner<\/li><li>Text::Autoformat<\/li><li>Text::CSV<\/li><li>Text::CSV_XS<\/li><li>Text::Diff<\/li><li>Text::Format<\/li><li>Text::Glob<\/li><li>Text::Iconv<\/li><li>Text::Reform<\/li><li>Text::Scan<\/li><li>Text::Shellwords<\/li><li>Text::Table<\/li><li>Text::Template<\/li><li>Tie::DB_FileLock<\/li><li>Tie::DB_Lock<\/li><li>Tie::Hash::MultiValue<\/li><li>Tie::IxHash<\/li><li>Tie::ToObject<\/li><li>Tie::Watch<\/li><li>Time::Piece::MySQL<\/li><li>TimeDate<\/li><li>Tk<\/li><li>Tk::HistEntry<\/li><li>Tk::Pod<\/li><li>Tree::DAG_Node<\/li><li>Try::Tiny<\/li><li>Type::Tie<\/li><li>Type::Tiny<\/li><li>Type::Tiny::XS<\/li><li>Types::Serialiser<\/li><li>Unicode::LineBreak<\/li><li>Unicode::Map<\/li><li>Unicode::String<\/li><li>Unicode::UTF8<\/li><li>UNIVERSAL::can<\/li><li>UNIVERSAL::isa<\/li><li>UNIVERSAL::moniker<\/li><li>UNIVERSAL::require<\/li><li>URI<\/li><li>Variable::Magic<\/li><li>version<\/li><li>Want<\/li><li>WSRF::Lite<\/li><li>WWW::Mechanize<\/li><li>WWW::RobotRules<\/li><li>XML::Atom<\/li><li>XML::CanonicalizeXML<\/li><li>XML::CommonNS<\/li><li>XML::Compile<\/li><li>XML::Compile::Cache<\/li><li>XML::Compile::SOAP<\/li><li>XML::Compile::Tester<\/li><li>XML::Compile::WSDL11<\/li><li>XML::DOM<\/li><li>XML::DOM::XPath<\/li><li>XML::Filter::BufferText<\/li><li>XML::Handler::YAWriter<\/li><li>XML::LibXML<\/li><li>XML::LibXML::Simple<\/li><li>XML::LibXSLT<\/li><li>XML::Namespace<\/li><li>XML::NamespaceFactory<\/li><li>XML::NamespaceSupport<\/li><li>XML::Node<\/li><li>XML::Parser<\/li><li>XML::Parser::Lite<\/li><li>XML::Quote<\/li><li>XML::RegExp<\/li><li>XML::RSS<\/li><li>XML::SAX<\/li><li>XML::SAX::Base<\/li><li>XML::SAX::Expat<\/li><li>XML::SAX::Writer<\/li><li>XML::SemanticCompare<\/li><li>XML::SemanticDiff<\/li><li>XML::Simple<\/li><li>XML::Stream<\/li><li>XML::Twig<\/li><li>XML::Writer<\/li><li>XML::XPath<\/li><li>XML::XPathEngine<\/li><li>XML-DOM<\/li><li>YAML<\/li><li>YAML::LibYAML<\/li><li>YAML::Syck<\/li><li>YAML::Tiny<\/li><\/ol>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>General Freeware Bio Freeware R modules Ruby modules Python modules Perl 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