# This file is autogenerated. Do not edit! Source: debian-med Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: misc Priority: optional Build-Depends-Indep: blends-dev (>= 0.7.5~), Build-Depends: debhelper-compat (= 13) Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/blends-team/med Vcs-Git: https://salsa.debian.org/blends-team/med.git Rules-Requires-Root: no Package: med-tasks Architecture: all Depends: tasksel, ${misc:Depends} Description: Debian Med tasks for tasksel This package provides Debian Med tasks in tasksel. . These tasks are described in detail at https://blends.debian.org/med/tasks/ Package: med-config Architecture: all Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15) Conflicts: med-common Replaces: med-common Provides: med-common Description: Debian Med general config package This package provides the basic infrastructure of all metapackages assembled by the Debian Med team. . This metapackage provides common features shared between the different metapackages of the project. Moreover it introduces a method to handle a 'med' system users group using debconf. . The Debian Med Project include metapackages for different tasks, which are: * applications for microbiological research and support for development of biological applications * cloud computing in microbiological research * drug databases * dental surgery practice * epidemiology and medical statistics * image processing and support for imaging application development * pharmacological research * radiation oncology, diagnostic imaging and related fields * medical practice * psychological research and practice * rehabilitation * typesetting and publishing * miscellaneous tools . Each task is represented by a metapackage. Metapackages do not contain executable programs, but rather dependencies from other packages. This way you will conveniently get all free medical software which is available for Debian by simply installing the relevant metapackage Package: med-all Section: metapackages Architecture: all Depends: ${misc:Depends} Recommends: med-bio, med-bio-dev, med-statistics Suggests: med-cloud, med-data, med-dental, med-epi, med-his, med-imaging, med-imaging-dev, med-laboratory, med-oncology, med-pharmacy, med-physics, med-practice, med-psychology, med-research, med-tools, med-typesetting Description: Default selection of tasks for Debian Med This package is part of the Debian Med Pure Blend and installs all tasks for a default installation of this blend. Package: med-bio Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: abacas, abpoa, abyss, acedb-other, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, anfo, any2fasta, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, assembly-stats, assemblytics, atac, ataqv, atropos, augur, augustus, autodock, autodock-vina, autogrid, avogadro, axe-demultiplexer, baitfisher, bali-phy, ballview, bamclipper, bamkit, bamtools, bandage, barrnap, bbmap, bcalm, bcftools, beads, beagle, beast-mcmc, beast2-mcmc, bedops, bedtools, belvu, berkeley-express, bifrost, bio-eagle, bio-rainbow, bio-tradis, bio-vcf, bioawk, biobambam2, biosyntax, bitseq, blasr, blixem, bolt-lmm, bowtie, bowtie2, boxshade, bppphyview, bppsuite, brig, btllib-tools, busco, bustools, bwa, canu, cassiopee, cat-bat, cct, cd-hit, cdbfasta, centrifuge, cgview, changeo, chimeraslayer, chromhmm, chromimpute, cif-tools, circlator, circos, clearcut, clonalframe, clonalframeml, clonalorigin, clustalo, clustalw, clustalx, cnvkit, codonw, comet-ms, concavity, conservation-code, coot, covtobed, crac, csb, ctffind, cutadapt, cutesv, daligner, damapper, datamash, dawg, dazzdb, deblur, delly, density-fitness, dextractor, dialign, dialign-tx, diamond-aligner, discosnp, disulfinder, dnaclust, dnarrange, dotter, drop-seq-tools, dssp, dwgsim, e-mem, ea-utils, ecopcr, edtsurf, eigensoft, elph, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, emmax, estscan, examl, exonerate, fasta3, fastahack, fastani, fastaq, fastdnaml, fastlink, fastml, fastp, fastq-pair, fastqc, fastqtl, fasttree, ffindex, figtree, filtlong, fitgcp, flash, flexbar, flye, fml-asm, freebayes, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gatb-core, gbrowse, gdpc, gemma, genometester, genomethreader, genometools, genomicsdb-tools, gentle, gff2aplot, gff2ps, gffread, ggd-utils, ghemical, ghmm, glam2, gmap, grabix, graphlan, grinder, gromacs, gsort, gubbins, gwama, harvest-tools, hhsuite, hilive, hinge, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, idba, igblast, igor, igv, indelible, infernal, insilicoseq, ipig, iqtree, iva, jaligner, jalview, jellyfish, jellyfish1, jmodeltest, jmol, kalign, kallisto, kaptive, khmer, kineticstools, king-probe, kissplice, kleborate, kma, kmc, kmer, kmerresistance, kraken, kraken2, lagan, lamarc, lamassemble, lambda-align, lambda-align2, last-align, lastz, leaff, lefse, libpwiz-tools, librg-utils-perl, libvcflib-tools, lighter, loki, ltrsift, lucy, lumpy-sv, macs, macsyfinder, maffilter, mafft, malt, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, mcaller, mecat2, megadepth, megahit, megan-ce, melting, meryl, metabat, metaeuk, metaphlan, metastudent, mhap, microbegps, microbiomeutil, mindthegap, minexpert2, minia, miniasm, minimac4, minimap, minimap2, mipe, mira-assembler, mirtop, mlv-smile, mmb, mmseqs2, mosdepth, mothur, mptp, mrbayes, multiqc, mummer, murasaki | murasaki-mpi, muscle, muscle3, mustang, nanofilt, nanolyse, nanook, nanopolish, nanostat, nanosv, nast-ier, ncbi-acc-download, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, ngmlr, njplot, norsnet, norsp, ntcard, nxtrim, obitools, openms, optimir, pal2nal, paleomix, paml, paraclu, parasail, parsinsert, parsnp, patman, pbdagcon, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, pftools, phast, phipack, phybin, phylip, phylonium, phyml, physamp, phyutility, phyx, picard-tools, picopore, pigx-rnaseq, piler, pilercr, pilon, pinfish, pique, pirs, pizzly, placnet, plasmidid, plasmidomics, plasmidseeker, plast, plink, plink1.9, plink2, plip, poa, populations, porechop, poretools, pplacer, prank, predictnls, presto, prime-phylo, primer3, prinseq-lite, proalign, probabel, probalign, probcons, proda, prodigal, profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd-net, profphd-utils, proftmb, progressivemauve, prokka, proteinortho, prottest, provean, pscan-chip, pscan-tfbs, psortb, pullseq, pycoqc, pycorrfit, pyensembl, pyfastx, pymol, pyscanfcs, python3-biomaj3-daemon, python3-bioxtasraw, python3-cogent3, python3-emperor, python3-geneimpacts, python3-gffutils, python3-pairtools, python3-pybedtools, python3-sqt, python3-treetime, pyvcf, qcat, qcumber, qiime, qtltools, quicktree, quorum, qutemol, r-bioc-annotate, r-bioc-biostrings, r-bioc-cner, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geoquery, r-bioc-hilbertvis, r-bioc-htsfilter, r-bioc-impute, r-bioc-limma, r-bioc-megadepth, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-mofa, r-bioc-multiassayexperiment, r-bioc-mutationalpatterns, r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-rtracklayer, r-bioc-scater, r-bioc-tfbstools, r-cran-adegenet, r-cran-adephylo, r-cran-alakazam, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-kaos, r-cran-phangorn, r-cran-phytools, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-samr, r-cran-sdmtools, r-cran-seqinr, r-cran-seurat, r-cran-shazam, r-cran-spp, r-cran-tcr, r-cran-tigger, r-cran-treespace, r-cran-tsne, r-cran-vegan, r-cran-webgestaltr, r-cran-wgcna, r-other-ascat, r-other-mott-happy.hbrem, r-other-rajewsky-dropbead, racon, radiant, ragout, rambo-k, rampler, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, readucks, reapr, recan, relion, relion-gui, repeatmasker-recon, reprof, resfinder, rna-star, rnahybrid, roary, rockhopper, roguenarok, rsem, rtax, runcircos-gui, saint, salmid, salmon, sambamba, samblaster, samclip, samtools, savvy-util, scoary, scrappie, scrm, scythe, seaview, seer, segemehl, sepp, seqan-apps, seqan-needle, seqan-raptor, seqkit, seqmagick, seqprep, seqsero, seqtk, sga, shasta, shovill, sibelia, sibsim4, sickle, sigma-align, sim4, sim4db, simka, simkamin, ska, skesa, skewer, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snippy, snp-sites, snpeff, snpomatic, snpsift, soapaligner, soapdenovo, soapdenovo2, soapsnp, sortmerna, spaced, spades, spaln, spoa, sprai, spread-phy, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, stringtie, subread, suitename, sumaclust, sumatra, sumtrees, surankco, surpyvor, survivor, svim, swarm, sweed, t-coffee, tabix, tantan, terraphast, theseus, thesias, tiddit, tigr-glimmer, tipp, tm-align, tnseq-transit, toil, tombo, tophat-recondition, topp, toppred, tortoize, trace2dbest, tracetuner, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trf, trim-galore, trimmomatic, trinityrnaseq, tvc, twopaco, uc-echo, ugene, umap-learn, umis, uncalled, unicycler, unikmer, varna, vcfanno, vcftools, velvet | velvet-long, velvetoptimiser, veryfasttree, vg, virulencefinder, vmatch, vsearch, vt, wham-align, wigeon, wise, xpore, yaha, yanagiba, yanosim Suggests: acacia, adun.app, agat, amos-assembler, amoscmp, annovar, apollo, arachne, arb, arvados, asap, axparafit, axpcoords, bagpipe, bambus, bax2bam, bcbio, biceps, big-blast, bigsdb, bismark, blat, blimps-utils, blobology, braker, btk-core, cactus, caftools, card-rgi, catfishq, cdna-db, cellprofiler, cinema, cluster3, cmap, conda-package-handling, condetri, contrafold, contralign, copycat, covpipe, crossbow, crux-toolkit, cufflinks, cytoscape, dascrubber, dazzle, deepbinner, deepnano, dendroscope, diann, dnapi, e-hive, ecell, embassy-phylip, emboss-explorer, ensembl, ensembl-vep, estferret, euler-sr, euler2, exabayes, exalt, excavator, ffp, fieldbioinformatics, figaro, flappie, forester, forge, galaxy, gatk, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gerp++, getdata, glimmerhmm, gmv, gramalign, graphbin, graphmap2, haploview, hawkeye, htqc, hts-nim-tools, idefix, idseq-bench, illustrate, inspect, jbrowse, jigsaw, kempbasu, libhdf5-dev, libhnswlib-dev, lofreq, mach-haplotyper, mage2tab, maker2, manta, marginphase, martj, maude, maxd, medaka, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, migrate, minimus, mirbase, modeller, molekel, mosaik-aligner, mpsqed, mrs, msatfinder, mugsy, mummergpu, mview, nano-snakemake, nanocall, nanocomp, nanoplot, ncbi-magicblast, nextsv, ngila, ngsqctoolkit, nw-align, oases, obo-edit, oligoarrayaux, omegamap, oncofuse, operondb, optitype, paipline, pangolin, partigene, partitionfinder, patristic, pcma, pfaat, phagefinder, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pigx-scrnaseq, pipasic, plato, pomoxis, profit, profphd, prot4est, psipred, pssh2, pufferfish, purple, pyrophosphate-tools, python3-alignlib, python3-anndata, python3-cgecore, python3-cyvcf2, python3-deeptools, python3-deeptoolsintervals, python3-htseq, python3-intake, python3-loompy, python3-nanoget, python3-nanomath, python3-ncls, python3-orange, python3-py2bit, python3-pybel, python3-pychopper, python3-pyfaidx, python3-pyflow, python3-pyranges, python3-pyrle, python3-pysam, python3-tinyalign, q2-alignment, q2-composition, q2-cutadapt, q2-dada2, q2-deblur, q2-demux, q2-diversity, q2-emperor, q2-feature-classifier, q2-feature-table, q2-fragment-insertion, q2-gneiss, q2-longitudinal, q2-metadata, q2-phylogeny, q2-quality-control, q2-quality-filter, q2-sample-classifier, q2-taxa, q2-types, q2-vsearch, q2cli, q2templates, qtlcart, qtlreaper, qualimap, quast, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-beachmat, r-bioc-biocneighbors, r-bioc-biocsingular, r-bioc-bitseq, r-bioc-ctc, r-bioc-dnacopy, r-bioc-ensembldb, r-bioc-experimenthub, r-bioc-geneplotter, r-bioc-genomicalignments, r-bioc-genomicfiles, r-bioc-genomicranges, r-bioc-go.db, r-bioc-grohmm, r-bioc-gviz, r-bioc-isoformswitchanalyzer, r-bioc-mofa2, r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db, r-bioc-qusage, r-bioc-savr, r-bioc-singlecellexperiment, r-bioc-structuralvariantannotation, r-bioc-tximport, r-cran-amap, r-cran-biwt, r-cran-boolnet, r-cran-corrplot, r-cran-drinsight, r-cran-dynamictreecut, r-cran-epir, r-cran-fitdistrplus, r-cran-forecast, r-cran-gprofiler2, r-cran-minerva, r-cran-optimalcutpoints, r-cran-parmigene, r-cran-pheatmap, r-cran-qqman, r-cran-rcpphnsw, r-cran-rentrez, r-cran-sctransform, r-other-apmswapp, r-other-fastbaps, raxml-ng, rbs-finder, relion-cuda, relion-gui-cuda, repeatmasker, resfinder-db, roadtrips, roche454ace2caf, rosa, rose, rsat, sailfish, sap, science-workflow, seq-gen, seq-seq-pan, seqcluster, seqwish, sift, signalalign, sina, sistr, situs, solvate, sourmash, sparta, splitstree, ssaha, strap, strap-base, strelka, tab2mage, tacg, tandem-genotypes, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tn-seqexplorer, tophat, treebuilder3d, tripal, trnascan-se, twain, ufasta, umap, unc-fish, uniprime, varmatch, varscan, vdjtools, vienna-rna, viewmol, vmd, x-tandem-pipeline, zodiac-zeden Description: Debian Med bioinformatics packages This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences. Package: med-bio-dev Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: bio-tradis, biobambam2, bioperl, bioperl-run, biosquid, cwltool, gffread, goby-java, libace-perl, libai-fann-perl, libbambamc-dev, libbamtools-dev, libbigwig-dev, libbio-alignio-stockholm-perl, libbio-asn1-entrezgene-perl, libbio-chado-schema-perl, libbio-cluster-perl, libbio-coordinate-perl, libbio-das-lite-perl, libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-hts-perl, libbio-db-ncbihelper-perl, libbio-db-seqfeature-perl, libbio-eutilities-perl, libbio-featureio-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-samtools-perl, libbio-scf-perl, libbio-tools-phylo-paml-perl, libbio-tools-run-alignment-clustalw-perl, libbio-tools-run-alignment-tcoffee-perl, libbio-tools-run-remoteblast-perl, libbio-variation-perl, libbiojava-java, libbiojava6-java, libbioparser-dev, libblasr-dev, libbpp-core-dev, libbpp-phyl-dev, libbpp-phyl-omics-dev, libbpp-popgen-dev, libbpp-qt-dev, libbpp-raa-dev, libbpp-seq-dev, libbpp-seq-omics-dev, libcdk-java, libchado-perl, libcifpp-dev, libconsensuscore-dev, libdivsufsort-dev, libedlib-dev, libfast5-dev, libfastahack-dev, libffindex0-dev, libfml-dev, libgatbcore-dev, libgclib-dev, libgenome-dev, libgenome-model-tools-music-perl, libgenome-perl, libgenometools0-dev, libgff-dev, libgkarrays-dev, libgo-perl, libhdf5-dev, libhmsbeagle-dev, libhts-dev, libhtscodecs-dev, libhtsjdk-java, libjebl2-java, libjloda-java, libkmer-dev, libmems-dev, libminimap2-dev, libmuscle-dev, libncbi-vdb-dev, libncbi6-dev, libncl-dev, libngs-java, libnhgri-blastall-perl, libopenmm-dev, libopenms-dev, libpal-java, libparasail-dev, libpbbam-dev, libpbdata-dev, libpbihdf-dev, libpbseq-dev, libpdb-redo-dev, libpll-dev, libpwiz-dev, libqes-dev, librcsb-core-wrapper0-dev, librdp-taxonomy-tree-java, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast0-dev, librostlab3-dev, libsbml5-dev, libseqan2-dev, libseqan3-dev, libseqlib-dev, libslow5-dev, libsmithwaterman-dev, libsnp-sites1-dev, libsort-key-top-perl, libspoa-dev, libsrf-dev, libssm-dev, libssu-dev, libssw-dev, libssw-java, libstaden-read-dev, libstatgen-dev, libswiss-perl, libtabixpp-dev, libthread-pool-dev, libvcflib-dev, libvibrant6-dev, libwfa2-dev, libzerg-perl, libzerg0-dev, mcl, nim-hts-dev, nim-kexpr-dev, nim-lapper-dev, ont-fast5-api, pyfai, python3-airr, python3-anndata, python3-bcbio-gff, python3-bioframe, python3-biom-format, python3-biomaj3, python3-biopython, python3-biotools, python3-bx, python3-cgecore, python3-cigar, python3-cobra, python3-cogent3, python3-cooler, python3-corepywrap, python3-csb, python3-cutadapt, python3-cyvcf2, python3-deeptools, python3-deeptoolsintervals, python3-dendropy, python3-dnaio, python3-ete3, python3-fast5, python3-freecontact, python3-gfapy, python3-gffutils, python3-gtfparse, python3-htseq, python3-intervaltree-bio, python3-kineticstools, python3-loompy, python3-mirtop, python3-nanoget, python3-ngs, python3-pairix, python3-pangolearn, python3-parasail, python3-pbcommand, python3-pbconsensuscore, python3-pbcore, python3-peptidebuilder, python3-presto, python3-propka, python3-py2bit, python3-pyabpoa, python3-pyani, python3-pybedtools, python3-pybel, python3-pybigwig, python3-pyfaidx, python3-pyfastx, python3-pymummer, python3-pyranges, python3-pysam, python3-pyspoa, python3-pyvcf, python3-rdkit, python3-ruffus, python3-screed, python3-shasta, python3-skbio, python3-slow5, python3-sqt, python3-streamz, python3-tinyalign, python3-torch, python3-treetime, python3-unifrac, python3-wdlparse, r-bioc-biobase, r-cran-boolnet, r-cran-corrplot, r-cran-distory, r-cran-fitdistrplus, r-cran-forecast, r-cran-genetics, r-cran-gprofiler2, r-cran-haplo.stats, r-cran-phangorn, r-cran-pheatmap, r-cran-phylobase, r-cran-pscbs, r-cran-qqman, r-cran-rentrez, r-cran-rncl, r-cran-rnexml, r-cran-rotl, r-cran-samr, r-cran-sctransform, r-cran-seqinr, r-cran-seurat, r-cran-tsne, r-cran-vegan, r-cran-webgestaltr, ruby-bio, ruby-crb-blast, sbmltoolbox, snakemake, toil Suggests: bioclipse, capsule-nextflow, conda-package-handling, ctdconverter, cthreadpool-dev, cwlformat, cwltest, libargs-dev, libatomicqueue-dev, libbam-dev, libbbhash-dev, libbifrost-dev, libbiojava4-java, libbiosoup-dev, libbtllib-dev, libcapsule-maven-nextflow-java, libconcurrentqueue-dev, libdisorder-dev, libfast-perl, libforester-java, libfreecontact-dev, libfreecontact-doc, libfreecontact-perl, libgatk-bwamem-java, libgatk-bwamem-jni, libgatk-fermilite-java, libgatk-fermilite-jni, libgatk-native-bindings-java, libgenomicsdb-dev, libgenomicsdb-java, libicb-utils-java, libmaus2-dev, libmilib-java, libminimap-dev, libmmblib-dev, libmodhmm-dev, libnexml-java, libngs-sdk-dev, libpbcopper-dev, libqcpp-dev, librelion-dev, libroadrunner-dev, librostlab-blast-doc, librostlab-doc, libsavvy-dev, libsuma-dev, libsvmloc-dev, libswarm2-dev, libterraces-dev, libtfbs-perl, libvbz-hdf-plugin-dev, libxxsds-dynamic-dev, octace-bioinfo, python-biopython-doc, python3-alignlib, python3-bcbio, python3-bel-resources, python3-bioblend, python3-biopython-sql, python3-cgelib, python3-compclust, python3-conda-package-streaming, python3-consensuscore2, python3-ctdopts, python3-galaxy-lib, python3-intake, python3-joypy, python3-misopy, python3-ncls, python3-networkx, python3-pycosat, python3-pyflow, python3-roadrunner, python3-scanpy, python3-seqcluster, q2-alignment, q2-composition, q2-cutadapt, q2-dada2, q2-deblur, q2-demux, q2-diversity, q2-emperor, q2-feature-classifier, q2-feature-table, q2-fragment-insertion, q2-gneiss, q2-longitudinal, q2-metadata, q2-phylogeny, q2-quality-control, q2-quality-filter, q2-sample-classifier, q2-shogun, q2-taxa, q2-types, q2-vsearch, q2cli, q2cwl, q2lint, q2templates, qiime, r-bioc-affxparser, r-bioc-affy, r-bioc-affyio, r-bioc-altcdfenvs, r-bioc-annotate, r-bioc-annotationdbi, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-arrayexpress, r-bioc-biocgenerics, r-bioc-biocneighbors, r-bioc-biomart, r-bioc-biomformat, r-bioc-biostrings, r-bioc-biovizbase, r-bioc-bitseq, r-bioc-bridgedbr, r-bioc-bsgenome, r-bioc-cager, r-bioc-cner, r-bioc-complexheatmap, r-bioc-ctc, r-bioc-cummerbund, r-bioc-dada2, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-enrichedheatmap, r-bioc-ensembldb, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-genomeinfodb, r-bioc-genomicalignments, r-bioc-genomicfeatures, r-bioc-genomicranges, r-bioc-geoquery, r-bioc-go.db, r-bioc-graph, r-bioc-gseabase, r-bioc-gsva, r-bioc-gviz, r-bioc-hypergraph, r-bioc-impute, r-bioc-iranges, r-bioc-limma, r-bioc-makecdfenv, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-mofa, r-bioc-multiassayexperiment, r-bioc-nanostringqcpro, r-bioc-oligo, r-bioc-oligoclasses, r-bioc-org.hs.eg.db, r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-preprocesscore, r-bioc-purecn, r-bioc-qusage, r-bioc-rbgl, r-bioc-rentrez, r-bioc-rsamtools, r-bioc-rtracklayer, r-bioc-s4vectors, r-bioc-savr, r-bioc-shortread, r-bioc-snpstats, r-bioc-structuralvariantannotation, r-bioc-tfbstools, r-bioc-titancna, r-bioc-tximport, r-bioc-variantannotation, r-bioc-xvector, r-cran-adegenet, r-cran-adephylo, r-cran-amap, r-cran-biwt, r-cran-drinsight, r-cran-dt, r-cran-dynamictreecut, r-cran-fastcluster, r-cran-future.apply, r-cran-future.batchtools, r-cran-ica, r-cran-itertools, r-cran-kaos, r-cran-metap, r-cran-minerva, r-cran-natserv, r-cran-nmf, r-cran-optimalcutpoints, r-cran-parmigene, r-cran-pcapp, r-cran-proc, r-cran-rann, r-cran-rcpphnsw, r-cran-robustrankaggreg, r-cran-rocr, r-cran-rook, r-cran-rsvd, r-cran-shazam, r-cran-sitmo, r-cran-venndiagram, r-other-apmswapp, ruby-rgfa, vdjtools Description: Debian Med packages for development of bioinformatics applications This metapackage will install Debian packages which might be helpful for development of applications for biological research. Package: med-cloud Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: abyss, acedb-other, aevol, alien-hunter, altree, amap-align, ampliconnoise, anfo, aragorn, arden, autodock, autodock-vina, autogrid, bamtools, bedtools, bioperl, bioperl-run, biosquid, bowtie, bowtie2, boxshade, bwa, cassiopee, cd-hit, cdbfasta, circos, clearcut, clonalframe, clustalo, clustalw, concavity, conservation-code, datamash, dialign, dialign-tx, discosnp, disulfinder, dnaclust, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastqc, fasttree, fitgcp, flexbar, freecontact, gasic, genometools, gff2aplot, gff2ps, glam2, gmap, grinder, gromacs, hhsuite, hisat2, hmmer, idba, infernal, jellyfish, kalign, kissplice, last-align, loki, macs, mafft, mapsembler2, maq, melting, minia, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, muscle3, mustang, ncbi-epcr, ncbi-tools-bin, ncoils, neobio, paraclu, parsinsert, pdb2pqr, perm, phyml, phyutility, picard-tools, plink, plink1.9, plink2, poa, prank, prime-phylo, primer3, probabel, probcons, proda, prodigal, python3-biomaj3-cli, python3-biopython, python3-cogent3, qiime, r-bioc-edger, r-bioc-hilbertvis, r-cran-pvclust, r-cran-qtl, r-cran-vegan, r-other-mott-happy.hbrem, raster3d, readseq, rnahybrid, rtax, samtools, seqan-apps, sibsim4, sigma-align, sim4, smalt, snap, soapdenovo, soapdenovo2, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, vcftools, velvet, veryfasttree, wise Suggests: bagpipe, blast2, cufflinks, embassy-phylip, giira Description: Debian Med bioinformatics applications usable in cloud computing This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited. Package: med-data Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: python3-hl7 Suggests: drugref.org, freediams, freemedforms-freedata, oscar Description: Debian Med drug databases This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application. Package: med-dental Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: entangle, imagetooth Description: Debian Med packages related to dental practice This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice. Package: med-epi Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: python3-seirsplus, python3-torch, python3-treetime, r-cran-covid19us, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epiestim, r-cran-epir, r-cran-epitools, r-cran-incidence, r-cran-kernelheaping, r-cran-lexrankr, r-cran-prevalence, r-cran-seroincidence, r-cran-sf, r-cran-sjplot, r-cran-surveillance Suggests: chime, epifire, netepi-analysis, netepi-collection, python3-epimodels, r-cran-cmprsk, r-cran-covid19, r-cran-msm, repast, shiny-server, ushahidi Description: Debian Med epidemiology related packages This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Package: med-his Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: fis-gtm, orthanc-wsi Suggests: care2x, ewd-920, hkma-cms, ipath, openeyes, openmaxims, openmrs, oscar-mcmaster, patientos, tryton-modules-health, vista-foia, world-vista Description: Debian Med suggestions for Hospital Information Systems This metapackage contains dependencies for software and that could be useful ro run a Hospital Information System. While there is continuous work going on to package a ready to install system currently only preconditions are finished but hopefully helpful in hospitals anyway. Package: med-imaging Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: amide, ants, bart, bart-view, biosig-tools, camitk-imp, ctn, ctsim, dcm2niix, dcmtk, dicom3tools, dicomscope, gdf-tools, gwyddion, heudiconv, imagej, invesalius, ismrmrd-tools, king, libgdcm-tools, medcon, mia-tools, mialmpick, minc-tools, mricron, mrtrix3, nifti-bin, odil, odin, openslide-tools, orthanc, orthanc-wsi, pixelmed-apps, plastimatch, python3-dipy, python3-nibabel, python3-nipy, python3-nipype, python3-nitime, python3-pydicom, python3-pyxid, python3-surfer, sightcalibrator, sightviewer, sigviewer, teem-apps, tifffile, vrrender, vtk-dicom-tools, xmedcon Suggests: afni, bart-cuda, bioimagesuite, bioimagexd, blox, brainvisa, caret, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, crea, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, ginkgocadx, hid, illustrate, imagemagick, imagevis3d, imview, incf-nidash-oneclick-clients, insightapplications, isis, itksnap, jemris, jist, kradview, libdcm4che-java, lipsia, maris, mayam, medisnap, mesa-test-tools, mia-viewit, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, openmeeg-tools, opensourcepacs, openwalnut-qt4, orthanc-dicomweb, orthanc-gdcm, orthanc-imagej, orthanc-mysql, orthanc-neuro, orthanc-postgresql, orthanc-webviewer, paraview, piano, pngquant, pymeg, science-workflow, slicer, sofa-apps, stabilitycalc, stir, tempo, trimage, via-bin, visit, vmtk, voxbo, xnat Description: Debian Med image processing and visualization packages This metapackage will install Debian packages which might be useful in medical image processing and visualization. . On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows. Package: med-imaging-dev Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: cimg-dev, ctn-dev, gmic, libbart-dev, libbiosig-dev, libcamitk-dev, libcifti-dev, libedf-dev, libgdf-dev, libgiftiio-dev, libinsighttoolkit5-dev, libismrmrd-dev, libmaxflow-dev, libmdc2-dev, libmia-2.4-dev, libmialm-dev, libminc-dev, libnifti2-dev, libodil-dev, libopencv-dev, libopenigtlink-dev, libopenslide-dev, libpapyrus3-dev, libsight-dev, libteem-dev, libvigraimpex-dev, libvistaio-dev, libvolpack1-dev, libvtk-dicom-dev, libvtk9-dev, libxdf-dev, octave-bart, octave-dicom, octave-gdf, odin, python3-biosig, python3-bioxtasraw, python3-brian, python3-dcmstack, python3-dipy, python3-gdcm, python3-imageio, python3-mia, python3-mne, python3-nibabel, python3-nipy, python3-nipype, python3-nitime, python3-openslide, python3-pydicom, python3-pyxnat, python3-torchvision, python3-vigra Suggests: emokit, libbio-formats-java, libcamp-dev, libctk-dev, libeegdev-dev, libfreeimage-dev, libgdcm2-dev, libics-dev, liblimereg-dev, libmni-perllib-perl, libnifti-doc, libopenmeeg-dev, libopenslide-java, libvia-dev, libvmtk-dev, libxdffileio-dev, python-vmtk, tifffile Description: Debian Med image processing and visualization packages development This metapackage will install Debian packages which might be useful for developing applications for medical image processing and visualization. Package: med-laboratory Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: opencfu, orthanc-wsi Suggests: catissuesuite, openelis, openfreezer Description: Debian Med suggestions for medical laboratories This metapackage contains dependencies for software and that could be useful ro run a medical laboratory. Package: med-oncology Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: orthanc-wsi, simrisc Suggests: planunc, python3-dicompylercore, uw-prism Description: Debian Med packages for oncology This metapackage will install tools that are useful for radiation oncology. Package: med-pharmacy Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: chemtool, r-cran-dosefinding, r-cran-rpact Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research. Package: med-physics Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: biosig-tools, gdf-tools, octave, r-base Suggests: gate, libbiosig-dev, octave-biosig, openvibe, paw, paw++, paw-demos, python3-biosig, python3-multipletau Description: Debian Med packages for medical physicists This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields. Package: med-practice Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: entangle, gnumed-client, gnumed-server, libchipcard-tools, orthanc, orthanc-wsi, oscar, qrisk2, r-cran-medadherence Suggests: clearhealth, elementalclinic, elexis, freeb, freediams, freemed, freemedforms-emr, freeshim, ginkgocadx, libctapimkt1, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb Description: Debian Med packages for practice management This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice. Package: med-psychology Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: orthanc-neuro, praat, psignifit, psychopy, python3-bioxtasraw, r-cran-foreign, r-cran-psy, r-cran-psych, r-cran-psychometric, r-cran-psychotree, r-cran-psyphy Suggests: python-pyepl, python3-bids-validator, python3-bmtk, python3-pynwb, science-psychophysics Description: Debian Med packages for psychology This metapackage contains dependencies for a collection of software which might be helpful for psychological research. Package: med-research Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: r-cran-rpact Suggests: openclinica Description: Debian Med packages for medical research This metapackage will install tools that are useful for medical research. Package: med-statistics Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: r-bioc-edger, r-bioc-limma, r-bioc-multtest, r-bioc-qvalue, r-cran-ade4, r-cran-beeswarm, r-cran-pvclust, r-cran-randomforest, r-cran-rwave, r-cran-snowfall, r-cran-waveslim, r-cran-wavethresh Suggests: rstudio, science-statistics Description: Debian Med statistics This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care. Package: med-tools Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: cronometer, cycle, edfbrowser, galileo, hunspell-de-med, hunspell-en-med, nutsqlite, pcalendar, python3-fitbit, quitcount, r-cran-fitbitscraper, r-cran-fitcoach, wgerman-medical, workrave Suggests: entangle, goldencheetah, mencal, mssstest, nut-nutrition, oscar, pesco, pondus Description: Debian Med several tools This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health. Package: med-typesetting Section: metapackages Architecture: all Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: king, texlive-latex-extra, texlive-science Suggests: biber, bibus, jabref-plugin-oo, kbibtex, r-cran-qqman Description: Debian Med support for typesetting and publishing This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology.