Debian Med Project
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Summary
Biology Development
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.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks
Index of all tasks

Debian Med Biology Development packages

Official Debian packages with high relevance

bio-tradis
??? missing short description for package bio-tradis :-(
Versions of package bio-tradis
ReleaseVersionArchitectures
sid1.4.5+dfsg2-2all
forky1.4.5+dfsg2-2all
trixie1.4.5+dfsg2-2all
bookworm1.4.5+dfsg2-1all
bullseye1.4.5+dfsg2-1all
Popcon: 8 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Lars Barquist, Matthew Mayho, Carla Cummins, Amy K. Cain, Christine J. Boinett, Andrew J. Page, Gemma C. Langridge, Michael A. Quail, Jacqueline A. Keane and Julian Parkhill: The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. (PubMed,eprint) Bioinformatics 32(7):1109-1111 (2016)
Registry entries: Bio.tools  SciCrunch  Bioconda 
biobambam2
??? missing short description for package biobambam2 :-(
Versions of package biobambam2
ReleaseVersionArchitectures
sid2.0.185+ds-2amd64,loong64,ppc64el,riscv64
bullseye2.0.179+ds-1amd64,arm64,i386
bookworm2.0.185+ds-1amd64,arm64,i386,ppc64el
trixie2.0.185+ds-2amd64,ppc64el,riscv64
forky2.0.185+ds-2amd64,loong64,ppc64el,riscv64
upstream2.0.185-release-20221211202123
Popcon: 13 users (32 upd.)*
Newer upstream!
 License: DFSG free
Git
The package is enhanced by the following packages: multiqc
Please cite: German Tischler and Steven Leonard: biobambam: tools for read pair collation based algorithms on BAM files. (eprint) Source Code Biol Med. 9:13 (2014)
Registry entries: Bio.tools  SciCrunch  Bioconda 
bioperl
??? missing short description for package bioperl :-(
Versions of package bioperl
ReleaseVersionArchitectures
sid1.7.8-3all
bullseye1.7.7-2all
bookworm1.7.8-1all
trixie1.7.8-1all
forky1.7.8-3all
Debtags of package bioperl:
devellang:perl, library
fieldbiology, biology:bioinformatics
roledevel-lib, shared-lib
Popcon: 22 users (36 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson and Ewan Birney: The Bioperl toolkit: Perl modules for the life sciences. (PubMed,eprint) Genome Res. 12(10):1611-1618 (2002)
Registry entries: Bio.tools  SciCrunch  Bioconda 
bioperl-run
??? missing short description for package bioperl-run :-(
Versions of package bioperl-run
ReleaseVersionArchitectures
bullseye1.7.3-6all
sid1.7.3-14all
trixie1.7.3-13all
bookworm1.7.3-9all
Debtags of package bioperl-run:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
Popcon: 7 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: clustalw exonerate kalign mcl
biosquid
??? missing short description for package biosquid :-(
Versions of package biosquid
ReleaseVersionArchitectures
bookworm1.9g+cvs20050121-12amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.9g+cvs20050121-12amd64,arm64,armhf,i386
forky1.9g+cvs20050121-16amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.9g+cvs20050121-16amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.9g+cvs20050121-15.1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package biosquid:
fieldbiology, biology:bioinformatics
interfacecommandline
roleprogram
scopeutility
usecomparing, converting, editing
Popcon: 10 users (42 upd.)*
Versions and Archs
 License: DFSG free
Git
cwltool
??? missing short description for package cwltool :-(
Versions of package cwltool
ReleaseVersionArchitectures
bookworm3.1.20230209161050-1all
sid3.2.20260413085819-1all
trixie3.1.20250110105449-3all
bullseye3.0.20210124104916-3+deb11u1all
forky3.2.20260413085819-1all
Popcon: 55 users (147 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reye, Bogdan Gavrilović, Carole Goble and The CWL Community: Methods included: standardizing computational reuse and portability with the Common Workflow Language. Communications of the ACM 65(6):54-63 (2022)
Registry entries: SciCrunch  Bioconda 
gffread
??? missing short description for package gffread :-(
Versions of package gffread
ReleaseVersionArchitectures
bullseye0.12.1-4amd64,arm64,armhf,i386
trixie0.12.7-8amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky0.12.7-8amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid0.12.7-8amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm0.12.7-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.12.9
Popcon: 7 users (36 upd.)*
Newer upstream!
 License: DFSG free
Git
Registry entries: Bio.tools  Bioconda 
goby-java
??? missing short description for package goby-java :-(
Versions of package goby-java
ReleaseVersionArchitectures
sid3.3.1+dfsg2-12all
forky3.3.1+dfsg2-12all
trixie3.3.1+dfsg2-11all
bookworm3.3.1+dfsg2-9all
Popcon: 6 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libace-perl
??? missing short description for package libace-perl :-(
Versions of package libace-perl
ReleaseVersionArchitectures
bookworm1.92-11amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.92-14amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.92-14amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.92-12amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye1.92-10amd64,arm64,armhf,i386
Debtags of package libace-perl:
devellang:perl, library
fieldbiology
Popcon: 17 users (39 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Lincoln D. Stein and Jean Thierry-Mieg: Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases. (PubMed,eprint) Genome Research 8(12):1308-1315 (1998)
Registry entries: Bioconda 
libai-fann-perl
??? missing short description for package libai-fann-perl :-(
Versions of package libai-fann-perl
ReleaseVersionArchitectures
bullseye0.10-5amd64,arm64,armhf,i386
trixie0.10-5amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky0.10-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid0.10-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm0.10-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package libai-fann-perl:
devellang:perl, library
Popcon: 3 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
libbambamc-dev
??? missing short description for package libbambamc-dev :-(
Versions of package libbambamc-dev
ReleaseVersionArchitectures
bookworm0.0.50-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky0.0.50-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid0.0.50-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie0.0.50-6amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye0.0.50-4amd64,arm64,armhf,i386
Popcon: 1 users (43 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: Bioconda 
libbamtools-dev
??? missing short description for package libbamtools-dev :-(
Versions of package libbamtools-dev
ReleaseVersionArchitectures
trixie2.5.2+dfsg-6amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky2.5.3+dfsg-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid2.5.3+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm2.5.2+dfsg-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.5.1+dfsg-9amd64,arm64,armhf,i386
Popcon: 1 users (44 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Stromberg and Gabor T. Marth: BamTools: a C++ API and toolkit for analyzing and managing BAM files. (PubMed,eprint) Bioinformatics 27(12):1691-2 (2011)
Registry entries: Bio.tools  SciCrunch  Bioconda 
libbigwig-dev
??? missing short description for package libbigwig-dev :-(
Versions of package libbigwig-dev
ReleaseVersionArchitectures
bullseye0.4.4+dfsg-2amd64,arm64,armhf,i386
sid0.4.8+dfsg-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky0.4.8+dfsg-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie0.4.7+dfsg-3.1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm0.4.7+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 2 users (40 upd.)*
Versions and Archs
 License: DFSG free
Git
Registry entries: Bioconda 
libbio-alignio-stockholm-perl
??? missing short description for package libbio-alignio-stockholm-perl :-(
Versions of package libbio-alignio-stockholm-perl
ReleaseVersionArchitectures
bullseye1.7.3-2all
sid1.7.3-2all
forky1.7.3-2all
trixie1.7.3-2all
bookworm1.7.3-2all
Popcon: 2 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-asn1-entrezgene-perl
??? missing short description for package libbio-asn1-entrezgene-perl :-(
Versions of package libbio-asn1-entrezgene-perl
ReleaseVersionArchitectures
sid1.730-3all
bullseye1.730-2all
bookworm1.730-2all
trixie1.730-3all
forky1.730-3all
Debtags of package libbio-asn1-entrezgene-perl:
devellang:perl
fieldbiology
works-with-formatplaintext
Popcon: 7 users (38 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-chado-schema-perl
??? missing short description for package libbio-chado-schema-perl :-(
Versions of package libbio-chado-schema-perl
ReleaseVersionArchitectures
bullseye0.20000-3all
sid0.20000-3all
forky0.20000-3all
trixie0.20000-3all
bookworm0.20000-3all
Debtags of package libbio-chado-schema-perl:
devellang:perl, library
Popcon: 2 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-cluster-perl
??? missing short description for package libbio-cluster-perl :-(
Versions of package libbio-cluster-perl
ReleaseVersionArchitectures
bookworm1.7.3-6all
sid1.7.3-6all
forky1.7.3-6all
trixie1.7.3-6all
bullseye1.7.3-5all
Popcon: 6 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-coordinate-perl
??? missing short description for package libbio-coordinate-perl :-(
Versions of package libbio-coordinate-perl
ReleaseVersionArchitectures
bullseye1.7.1-4all
bookworm1.7.1-4all
trixie1.7.1-4all
forky1.7.1-4all
sid1.7.1-4all
Popcon: 7 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-das-lite-perl
??? missing short description for package libbio-das-lite-perl :-(
Versions of package libbio-das-lite-perl
ReleaseVersionArchitectures
bullseye2.11-8all
sid2.11-9all
forky2.11-9all
trixie2.11-9all
bookworm2.11-8all
Debtags of package libbio-das-lite-perl:
devellang:perl, library
Popcon: 3 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-db-biofetch-perl
??? missing short description for package libbio-db-biofetch-perl :-(
Versions of package libbio-db-biofetch-perl
ReleaseVersionArchitectures
forky1.7.3-4all
bookworm1.7.3-4all
bullseye1.7.3-4all
sid1.7.3-4all
trixie1.7.3-4all
Popcon: 4 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-db-embl-perl
??? missing short description for package libbio-db-embl-perl :-(
Versions of package libbio-db-embl-perl
ReleaseVersionArchitectures
forky1.7.4-4all
trixie1.7.4-4all
bookworm1.7.4-4all
bullseye1.7.4-4all
sid1.7.4-4all
Popcon: 2 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-db-hts-perl
??? missing short description for package libbio-db-hts-perl :-(
Versions of package libbio-db-hts-perl
ReleaseVersionArchitectures
bookworm3.01-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie3.01-5amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky3.01-6amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid3.01-6amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye3.01-3amd64,arm64,armhf,i386
Popcon: 0 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-db-ncbihelper-perl
??? missing short description for package libbio-db-ncbihelper-perl :-(
Versions of package libbio-db-ncbihelper-perl
ReleaseVersionArchitectures
forky1.7.8-1all
trixie1.7.8-1all
bullseye1.7.6-4all
bookworm1.7.7-1all
sid1.7.8-1all
Popcon: 36 users (27 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-db-seqfeature-perl
??? missing short description for package libbio-db-seqfeature-perl :-(
Versions of package libbio-db-seqfeature-perl
ReleaseVersionArchitectures
forky1.7.5-1all
bullseye1.7.4-1all
bookworm1.7.4-2all
trixie1.7.5-1all
sid1.7.5-1all
Popcon: 91 users (24 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-eutilities-perl
??? missing short description for package libbio-eutilities-perl :-(
Versions of package libbio-eutilities-perl
ReleaseVersionArchitectures
forky1.77-3all
sid1.77-3all
bullseye1.77-1all
bookworm1.77-2all
trixie1.77-3all
Popcon: 17 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-featureio-perl
??? missing short description for package libbio-featureio-perl :-(
Versions of package libbio-featureio-perl
ReleaseVersionArchitectures
trixie1.6.905-2all
bullseye1.6.905-2all
sid1.6.905-2all
forky1.6.905-2all
bookworm1.6.905-2all
Popcon: 6 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-graphics-perl
??? missing short description for package libbio-graphics-perl :-(
Versions of package libbio-graphics-perl
ReleaseVersionArchitectures
forky2.40-7all
bullseye2.40-6all
bookworm2.40-6all
trixie2.40-6all
sid2.40-7all
Debtags of package libbio-graphics-perl:
devellang:perl, library
fieldbiology, biology:bioinformatics
roleshared-lib
Popcon: 94 users (24 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-mage-perl
??? missing short description for package libbio-mage-perl :-(
Versions of package libbio-mage-perl
ReleaseVersionArchitectures
trixie20030502.3-6all
sid20030502.3-6all
bullseye20030502.3-6all
bookworm20030502.3-6all
forky20030502.3-6all
Debtags of package libbio-mage-perl:
fieldbiology, biology:bioinformatics
roledevel-lib
Popcon: 3 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-mage-utils-perl
??? missing short description for package libbio-mage-utils-perl :-(
Versions of package libbio-mage-utils-perl
ReleaseVersionArchitectures
trixie20030502.0-5all
bullseye20030502.0-5all
bookworm20030502.0-5all
forky20030502.0-5all
sid20030502.0-5all
Debtags of package libbio-mage-utils-perl:
fieldbiology, biology:bioinformatics
Popcon: 3 users (35 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-primerdesigner-perl
??? missing short description for package libbio-primerdesigner-perl :-(
Versions of package libbio-primerdesigner-perl
ReleaseVersionArchitectures
sid0.07-8all
bullseye0.07-8all
trixie0.07-8all
bookworm0.07-8all
forky0.07-8all
Debtags of package libbio-primerdesigner-perl:
devellang:perl, library
roleshared-lib
Popcon: 5 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-samtools-perl
??? missing short description for package libbio-samtools-perl :-(
Versions of package libbio-samtools-perl
ReleaseVersionArchitectures
bullseye1.43-3amd64,arm64,armhf,i386
bookworm1.43-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.43-5amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.43-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.43-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package libbio-samtools-perl:
devellang:perl, library
roleshared-lib
Popcon: 7 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-scf-perl
??? missing short description for package libbio-scf-perl :-(
Versions of package libbio-scf-perl
ReleaseVersionArchitectures
bookworm1.03-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.03-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.03-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie1.03-7amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye1.03-5amd64,arm64,armhf,i386
Debtags of package libbio-scf-perl:
devellang:perl, library
roleshared-lib
Popcon: 0 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-tools-phylo-paml-perl
??? missing short description for package libbio-tools-phylo-paml-perl :-(
Versions of package libbio-tools-phylo-paml-perl
ReleaseVersionArchitectures
bullseye1.7.3-3all
trixie1.7.3-4all
bookworm1.7.3-4all
sid1.7.3-4all
Popcon: 4 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-tools-run-alignment-clustalw-perl
??? missing short description for package libbio-tools-run-alignment-clustalw-perl :-(
Versions of package libbio-tools-run-alignment-clustalw-perl
ReleaseVersionArchitectures
sid1.7.4-4all
bookworm1.7.4-3all
trixie1.7.4-4all
bullseye1.7.4-2all
Popcon: 5 users (36 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-tools-run-alignment-tcoffee-perl
??? missing short description for package libbio-tools-run-alignment-tcoffee-perl :-(
Versions of package libbio-tools-run-alignment-tcoffee-perl
ReleaseVersionArchitectures
bullseye1.7.4-2all
sid1.7.4-3all
trixie1.7.4-3all
bookworm1.7.4-3all
Popcon: 2 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-tools-run-remoteblast-perl
??? missing short description for package libbio-tools-run-remoteblast-perl :-(
Versions of package libbio-tools-run-remoteblast-perl
ReleaseVersionArchitectures
trixie1.7.3-3all
bookworm1.7.3-3all
bullseye1.7.3-3all
sid1.7.3-3all
forky1.7.3-3all
Popcon: 7 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbio-variation-perl
??? missing short description for package libbio-variation-perl :-(
Versions of package libbio-variation-perl
ReleaseVersionArchitectures
forky1.7.5-3all
trixie1.7.5-3all
bookworm1.7.5-3all
sid1.7.5-3all
bullseye1.7.5-2all
Popcon: 13 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbiojava-java
??? missing short description for package libbiojava-java :-(
Versions of package libbiojava-java
ReleaseVersionArchitectures
forky1.9.7+dfsg-2all
bullseye1.7.1-9all
bookworm1.9.5+dfsg-3all
sid1.9.7+dfsg-2all
trixie1.9.7+dfsg-2all
Debtags of package libbiojava-java:
devellang:java, library
fieldbiology, biology:bioinformatics
roledevel-lib
Popcon: 17 users (33 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: R. C. G. Holland, T. Down, M. Pocock, A. Prlićand D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer and M. J. Schreiber: BioJava: an Open-Source Framework for Bioinformatics. (PubMed,eprint) Bioinformatics 24(18):2096-2097 (2008)
Registry entries: Bio.tools 
libbiojava6-java
??? missing short description for package libbiojava6-java :-(
Versions of package libbiojava6-java
ReleaseVersionArchitectures
bookworm6.1.0+dfsg-4all
sid6.1.0+dfsg-6all
forky6.1.0+dfsg-6all
trixie6.1.0+dfsg-5all
Popcon: 9 users (37 upd.)*
Versions and Archs
 License: DFSG free
Git
libbioparser-dev
??? missing short description for package libbioparser-dev :-(
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libbpp-core-dev
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libbpp-phyl-dev
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libbpp-phyl-omics-dev
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libbpp-popgen-dev
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libbpp-seq-dev
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libbpp-seq-omics-dev
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libcdk-java
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libcifpp-dev
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libconsensuscore-dev
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libdivsufsort-dev
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libedlib-dev
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libfast5-dev
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libfml-dev
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libgatbcore-dev
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Please cite: Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo and Dominique Lavenier: GATB: Genome Assembly & Analysis Tool Box. Bioinformatics 30(20):2959-2961 (2014)
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libgenome-dev
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libgenome-model-tools-music-perl
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libgenome-perl
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libgenometools0-dev
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Please cite: Gordon Gremme, Sascha Steinbiss and Stefan Kurtz: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.. (PubMed) IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(3):645-656 (2013)
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libgkarrays-dev
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Please cite: Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes and Eric Rivals: Querying large read collections in main memory: a versatile data structure. (PubMed) BMC Bioinformatics 12:242 (2011)
libgo-perl
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libhdf5-dev
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libhmsbeagle-dev
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Please cite: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. (PubMed,eprint) Systematic Biology 61(1):170-3 (2012)
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libhts-dev
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Please cite: Heng Li: Tabix: fast retrieval of sequence features from generic TAB-delimited files. (PubMed,eprint) Bioinformatics 27(5):718-719 (2011)
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libhtscodecs-dev
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libhtsjdk-java
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libjebl2-java
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Remark of Debian Med team: Fork from jebl

This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library.
libjloda-java
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Please cite: Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause and Daniel H. Huson: MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman. (eprint) bioRxiv (2016)
libkmer-dev
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Please cite: B. Walenz and L. Florea: Sim4db and leaff: Utilities for fast batched spliced alignment and sequence indexing. (PubMed) Bioinformatics 27(13):1869-1870 (2011)
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libmems-dev
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libminimap2-dev
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Please cite: Heng Li: Minimap2: pairwise alignment for nucleotide sequences. (PubMed,eprint) Bioinformatics :2103-2110 (2018)
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libmmblib-dev
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libmuscle-dev
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libncbi6-dev
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libncl-dev
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Please cite: Paul O. Lewis: NCL: a C++ class library for interpreting data files in NEXUS format. (PubMed,eprint) Bioinformatics 19(17):2330-2331 (2003)
libngs-java
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libngs-sdk-dev
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libnhgri-blastall-perl
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libopenmm-dev
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Please cite: P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks and V. S. Pande: OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. (PubMed,eprint) PLOS Comp. Biol. 13(7):e1005659 (2017)
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libopenms-dev
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Please cite: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher: OpenMS – an Open-Source Software Framework for Mass Spectrometry. (PubMed,eprint) BMC Bioinformatics 9(163) (2008)
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libpal-java
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Please cite: Alexei Drummond and Korbinian Strimmer: PAL: an object-oriented programming library for molecular evolution and phylogenetics. (PubMed,eprint) Bioinformatics 17(7):662-663 (2001)
libparasail-dev
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libpbbam-dev
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libpbdata-dev
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libpbihdf-dev
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libpbseq-dev
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libpdb-redo-dev
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libpll-dev
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libpwiz-dev
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libqes-dev
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librcsb-core-wrapper0-dev
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librdp-taxonomy-tree-java
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librg-blast-parser-perl
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librg-reprof-bundle-perl
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librostlab-blast0-dev
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Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)
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Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)
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libsnp-sites1-dev
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Please cite: Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane and Simon R. Harris: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. (eprint) Microbial Genomics 2(4) (2016)
libsort-key-top-perl
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libssm-dev
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Please cite: E. Krissinel and K. Henrick: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. (PubMed,eprint) Acta Crystallogr D Biol Crystallogr. 60(1):2256-68 (2004)
libssu-dev
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Please cite: Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez and Rob Knight: Striped UniFrac: enabling microbiome analysis at unprecedented scale. (PubMed) Nature Methods 15(11):847–848 (2018)
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libssw-java
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libstaden-read-dev
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libstatgen-dev
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libswiss-perl
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libthread-pool-dev
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libvcflib-dev
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libvibrant6-dev
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libzerg-perl
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libzerg0-dev
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mcl
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The package is enhanced by the following packages: zoem
Please cite: Stijn van Dongen and Cei Abreu-Goodger: Using MCL to extract clusters from networks. (PubMed,eprint) Methods Mol Biol. 804:281-95 (2012)
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nim-hts-dev
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The package is enhanced by the following packages: nim-hts-examples
nim-kexpr-dev
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nim-lapper-dev
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ont-fast5-api
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python3-airr
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python3-anndata
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Please cite: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis: SCANPY: large-scale single-cell gene expression data analysis.. (PubMed) Genome Biol. 19:15 (2018)
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python3-biom-format
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python3-biomaj3
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python3-biopython
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Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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python3-biotools
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Please cite: Rebecca Bart, Megan Cohn, Andrew Kassen, Emily J. McCallum, Mikel Shybut, Annalise Petriello, Ksenia Krasileva, Douglas Dahlbeck, Cesar Medina, Titus Alicai, Lava Kumar, Leandro M. Moreira, Júlio Rodrigues Neto, Valerie Verdier, María Angélica Santana, Nuttima Kositcharoenkul, Hervé Vanderschuren, Wilhelm Gruissem, Adriana Bernal and Brian J. Staskawicz: High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. (PubMed) PNAS 109(28):E1972-9 (2012)
python3-bx
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python3-cigar
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Please cite: Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson and Daniel R Hyduke: COBRApy: COnstraints-Based Reconstruction and Analysis for Python. (PubMed) BMC Systems Biology 7(74) (2013)
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python3-cogent3
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Please cite: Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying and Gavin A Huttley: PyCogent: a toolkit for making sense from sequence. (PubMed,eprint) Genome Biology 8(8):R171 (2007)
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python3-cooler
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The package is enhanced by the following packages: python3-cooler-examples
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python3-corepywrap
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python3-csb
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python3-cutadapt
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Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. (eprint) EMBnet.journal 17(1):10-12 (2015)
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python3-cyvcf2
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Please cite: Brent S. Pedersen and Aaron R. Quinlan: cyvcf2: fast, flexible variant analysis with Python. (eprint) Bioinformatics 33(12):1867–1869 (2017)
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python3-deeptools
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Please cite: Fidel Ramirez, Devon P. Ryan, Björn Grüning, Sarah Diehl, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar and Thomas Manke: deepTools2: a next generation web server for deep-sequencing data analysis. (eprint) Nucleic Acids Research :W160–W165 (2016)
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python3-deeptoolsintervals
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python3-dendropy
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Please cite: Jeet Sukumaran and Mark T. Holder: DendroPy: a Python library for phylogenetic computing. (PubMed,eprint) Bioinformatics 26(12):1569-1571 (2010)
python3-dnaio
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python3-ete3
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Please cite: Jaime Huerta-Cepas, François Serra and Peer Bork: ETE 3: Reconstruction analysis and visualization of phylogenomic data. (eprint) Mol. Biol. Evol. (2016)
python3-fast5
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python3-freecontact
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Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
python3-gfapy
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Please cite: Giorgio Gonnella and Stefan Kurtz: GfaPy: a flexible and extensible software library for handling sequence graphs in Python. (PubMed) Bioinformatics (2017)
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python3-gffutils
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python3-gtfparse
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python3-htseq
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Please cite: Simon Anders, Paul Theodor Pyl and Wolfgang Huber: HTSeq—a Python framework to work with high-throughput sequencing data. (PubMed,eprint) Bioinformatics 31(2):166-169 (2015)
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python3-intervaltree-bio
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python3-kineticstools
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python3-loompy
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python3-mirtop
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Please cite: Thomas Desvignes, Karen Eilbeck, Ioannis S. Vlachos, Bastian Fromm, Yin Lu, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese, Elisa Ficarra, Shruthi Bandyadka, Jason Sydes, Peter Batzel, John H. Postlethwait, Phillipe Loher, Eric Londin, Aristeidis G. Telonis, Isidore Rigoutsos and Lorena Pantano Rubino: miRTOP: An open source community project for the development of a unified format file for miRNA data [version 1; not peer reviewed]. (eprint) F1000Research 7(ISCB Comm. J.):953 (Slides) (2018)
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python3-nanoget
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python3-ngs
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python3-pairix
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python3-pangolearn
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python3-pbcore
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python3-peptidebuilder
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Please cite: Matthew Z. Tien, Dariya K. Sydykova, Austin G. Meyer and Claus O. Wilke: PeptideBuilder: A simple Python library to generate model peptides. (PubMed,eprint) PeerJ 1:e80 (2013)
python3-presto
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Please cite: Chresten R. Søndergaard, Mats H. M. Olsson, Michał Rostkowski and Jan H. Jensen: Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. Journal of Chemical Theory and Computation 7(7):2284–2295 (2011)
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python3-pyfaidx
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The package is enhanced by the following packages: python-pysam-tests
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Please cite: Leo Goodstadt: Ruffus: A Lightweight Python Library for Computational Pipelines. (PubMed,eprint) Bioinformatics 26(21):2778-9 (2010)
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Please cite: K. Shafin, T. Pesout and R. Lorig-Roach et al.: Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology (2020)
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python3-sqt
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python3-tinyalign
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r-bioc-biobase
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Please cite: Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean Y H Yang and Jianhua Zhang: Bioconductor: Open software development for computational biology and bioinformatics. (PubMed,eprint) Genome Biology 5(10):R80 (2004)
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Remark of Debian Med team: This is a part of Bioconductor project

A nice overview about all modules of BioDonductor is given at http://www.bioconductor.org/packages/release/bioc/
r-cran-boolnet
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Please cite: Christoph Muessel, Martin Hopfensitz and Hans A. Kestler: BoolNet -- an R package for generation, reconstruction and analysis of Boolean networks. (eprint) Bioinformatics 26(6):1378-1380 (2010)
r-cran-corrplot
??? missing short description for package r-cran-corrplot :-(
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r-cran-distory
??? missing short description for package r-cran-distory :-(
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r-cran-fitdistrplus
??? missing short description for package r-cran-fitdistrplus :-(
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Please cite: Marie Laure Delignette-Muller Christophe Dutang: fitdistrplus: An R Package for Fitting Distributions. Journal of Statistical Software 64(4):1-34 (2015)
r-cran-forecast
??? missing short description for package r-cran-forecast :-(
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r-cran-genetics
??? missing short description for package r-cran-genetics :-(
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r-cran-gprofiler2
??? missing short description for package r-cran-gprofiler2 :-(
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r-cran-haplo.stats
??? missing short description for package r-cran-haplo.stats :-(
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r-cran-phangorn
??? missing short description for package r-cran-phangorn :-(
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Please cite: K.P. Schliep: phangorn: phylogenetic analysis in R. (PubMed) Bioinformatics 27(4):592-593 (2011)
r-cran-pheatmap
??? missing short description for package r-cran-pheatmap :-(
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r-cran-phylobase
??? missing short description for package r-cran-phylobase :-(
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r-cran-pscbs
??? missing short description for package r-cran-pscbs :-(
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Please cite: Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen and Venkatraman E. Seshan: Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. (PubMed,eprint) Bioinformatics 27(15):2038-2046 (2011)
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r-cran-qqman
??? missing short description for package r-cran-qqman :-(
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Please cite: Stephen D. Turner: qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. (eprint) bioRxiv (2014)
r-cran-rentrez
??? missing short description for package r-cran-rentrez :-(
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r-cran-rncl
??? missing short description for package r-cran-rncl :-(
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r-cran-rnexml
??? missing short description for package r-cran-rnexml :-(
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r-cran-rotl
??? missing short description for package r-cran-rotl :-(
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r-cran-samr
??? missing short description for package r-cran-samr :-(
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r-cran-sctransform
??? missing short description for package r-cran-sctransform :-(
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r-cran-seqinr
??? missing short description for package r-cran-seqinr :-(
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Please cite: Delphine Charif and Jean R. Lobry: SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. :207-232 (2007)
r-cran-seurat
??? missing short description for package r-cran-seurat :-(
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Please cite: Rahul Satija, Jeffrey A. Farrell, David Gennert, Alexander F. Schier and Aviv Regev: Spatial reconstruction of single-cell gene expression data. (PubMed) Nature Biotechnology 33:495–502 (2015)
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r-cran-tsne
??? missing short description for package r-cran-tsne :-(
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r-cran-vegan
??? missing short description for package r-cran-vegan :-(
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r-cran-webgestaltr
??? missing short description for package r-cran-webgestaltr :-(
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ruby-bio
??? missing short description for package ruby-bio :-(
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ruby-crb-blast
??? missing short description for package ruby-crb-blast :-(
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sbmltoolbox
??? missing short description for package sbmltoolbox :-(
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Please cite: S. M. Keating, B. J. Bornstein, A. Finney and M. Hucka: SBMLToolbox: an SBML toolbox for MATLAB users.. (eprint) Bioinformatics 22(10):1275-1277 (2006)
Screenshots of package sbmltoolbox
snakemake
??? missing short description for package snakemake :-(
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Please cite: Johannes Köster and Sven Rahmann: Snakemake-a scalable bioinformatics workflow engine. Bioinformatics (2012)
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toil
??? missing short description for package toil :-(
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Please cite: John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten: Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology 35(4):314–316 (2017)
Registry entries: Bioconda 

Official Debian packages with lower relevance

capsule-nextflow
??? missing short description for package capsule-nextflow :-(
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conda-package-handling
??? missing short description for package conda-package-handling :-(
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ctdconverter
??? missing short description for package ctdconverter :-(
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cthreadpool-dev
??? missing short description for package cthreadpool-dev :-(
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cwlformat
??? missing short description for package cwlformat :-(
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cwltest
??? missing short description for package cwltest :-(
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Please cite: Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić, Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes and Luka Stojanovic: Common Workflow Language, v1.0. (2016)
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libargs-dev
??? missing short description for package libargs-dev :-(
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libbam-dev
??? missing short description for package libbam-dev :-(
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Please cite: Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map (SAM) Format and SAMtools. (PubMed,eprint) Bioinformatics 25(16):2078-2079 (2009)
libbbhash-dev
??? missing short description for package libbbhash-dev :-(
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Please cite: Antoine Limasset, Guillaume Rizk, Rayan Chikhi and Pierre Peterlongo: Fast and scalable minimal perfect hashing for massive key sets. HAL-Inria (2017)
libbifrost-dev
??? missing short description for package libbifrost-dev :-(
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Please cite: Guillaume Holley and Páll Melsted: Bifrost – Highly parallel construction and indexing of colored and compacted de Bruijn graphs. (PubMed,eprint) bioRxiv 21(1):249 (2020)
Registry entries: Bio.tools  Bioconda 
libbiojava4-java
??? missing short description for package libbiojava4-java :-(
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libbiosoup-dev
??? missing short description for package libbiosoup-dev :-(
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libbtllib-dev
??? missing short description for package libbtllib-dev :-(
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Please cite: Vladimir Nikolić, Parham Kazemi, Lauren Coombe, Johnathan Wong, Amirhossein Afshinfard, Justin Chu, René L. Warren and Inanç Birol: btllib: A C++ library with Python interface for efficient genomic sequence processing. (eprint) Journal of Open Source Software 7(79) (2022)
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Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics (2014)
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Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics (2014)
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Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: fast and free software for protein contact prediction from residue co-evolution.. (PubMed,eprint) BMC Bioinformatics 15:85 (2014)
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Please cite: Heng Li: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. (eprint) Bioinformatics :2103-2110 (2016)
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libterraces-dev
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Please cite: Michael J. Sanderson, Michelle M. McMahon and Mike Steel: Terraces in phylogenetic tree space. (PubMed) Science 333(6041):448-450 (2011)
libtfbs-perl
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libxxsds-dynamic-dev
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python-biopython-doc
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Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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python3-biopython-sql
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Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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python3-ncls
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Please cite: Endre Bakken Stovner and Pål Sætrom: PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918–919 (2020)
python3-networkx
??? missing short description for package python3-networkx :-(
Versions of package python3-networkx
ReleaseVersionArchitectures
sid3.4.2-5all
trixie3.2.1-5all
bullseye2.5+ds-2all
bookworm2.8.8-1all
forky3.4.2-5all
upstream3.6.1
Popcon: 974 users (858 upd.)*
Newer upstream!
 License: DFSG free
Git
python3-pycosat
??? missing short description for package python3-pycosat :-(
Versions of package python3-pycosat
ReleaseVersionArchitectures
forky0.6.6+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid0.6.6+dfsg-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie0.6.6+dfsg-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm0.6.4+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.6.3+dfsg-1amd64,arm64,armhf,i386
Popcon: 6 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
python3-pyflow
??? missing short description for package python3-pyflow :-(
Versions of package python3-pyflow
ReleaseVersionArchitectures
bullseye1.1.20-2amd64,arm64,armhf,i386
bookworm1.1.20-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 1 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
q2-alignment
??? missing short description for package q2-alignment :-(
Versions of package q2-alignment
ReleaseVersionArchitectures
bookworm2022.11.1-2all
bullseye2020.11.1-2all
sid2024.5.0-1all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-cutadapt
??? missing short description for package q2-cutadapt :-(
Versions of package q2-cutadapt
ReleaseVersionArchitectures
sid2024.5.0-1amd64,arm64,loong64,ppc64el,riscv64
bookworm2022.11.1-2amd64,arm64,mips64el,ppc64el
bullseye2020.11.1-1amd64,arm64
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-dada2
??? missing short description for package q2-dada2 :-(
Versions of package q2-dada2
ReleaseVersionArchitectures
bullseye2020.11.1-3amd64
bookworm2022.11.2-2amd64
sid2024.5.0-1amd64
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-demux
??? missing short description for package q2-demux :-(
Versions of package q2-demux
ReleaseVersionArchitectures
sid2024.5.0+dfsg-1all
bullseye2020.11.1-1all
bookworm2022.11.1+dfsg-2all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-emperor
??? missing short description for package q2-emperor :-(
Versions of package q2-emperor
ReleaseVersionArchitectures
bookworm2022.11.1-2all
sid2024.5.0-2all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-feature-classifier
??? missing short description for package q2-feature-classifier :-(
Versions of package q2-feature-classifier
ReleaseVersionArchitectures
bullseye2020.11.1-2all
bookworm2022.11.1-2all
sid2024.5.0-1all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
Registry entries: Bio.tools 
q2-feature-table
??? missing short description for package q2-feature-table :-(
Versions of package q2-feature-table
ReleaseVersionArchitectures
bookworm2022.11.1+dfsg-2all
sid2024.5.0+dfsg-1all
bullseye2020.11.1+dfsg-1all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-fragment-insertion
??? missing short description for package q2-fragment-insertion :-(
Versions of package q2-fragment-insertion
ReleaseVersionArchitectures
bookworm2022.11.1-3amd64,arm64,mips64el,ppc64el
sid2024.5.0-1amd64,arm64,loong64,ppc64el,riscv64
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-metadata
??? missing short description for package q2-metadata :-(
Versions of package q2-metadata
ReleaseVersionArchitectures
sid2024.5.0+dfsg-1amd64,arm64,loong64,ppc64el,riscv64
bookworm2022.8.0-1amd64,arm64,mips64el,ppc64el
bullseye2020.11.1+dfsg-1amd64,arm64
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-phylogeny
??? missing short description for package q2-phylogeny :-(
Versions of package q2-phylogeny
ReleaseVersionArchitectures
sid2024.5.0-1amd64
bookworm2022.11.1-3amd64
experimental2022.11.1-1all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
q2-quality-control
??? missing short description for package q2-quality-control :-(
Versions of package q2-quality-control
ReleaseVersionArchitectures
bookworm2022.11.1-2all
sid2024.5.0-2all
bullseye2020.11.1-3all
upstream2026.4.0
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-quality-filter
??? missing short description for package q2-quality-filter :-(
Versions of package q2-quality-filter
ReleaseVersionArchitectures
sid2024.5.0-1all
bookworm2022.11.1-2all
bullseye2020.11.1-2all
upstream2026.4.0
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 License: DFSG free
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-sample-classifier
??? missing short description for package q2-sample-classifier :-(
Versions of package q2-sample-classifier
ReleaseVersionArchitectures
bullseye2020.11.1-3all
sid2024.5.0-2all
bookworm2022.11.1-3all
upstream2026.4.0
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 License: DFSG free
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Registry entries: Bio.tools 
q2-taxa
??? missing short description for package q2-taxa :-(
Versions of package q2-taxa
ReleaseVersionArchitectures
bullseye2020.11.1+dfsg-2all
bookworm2022.11.1+dfsg-2all
sid2024.5.0+dfsg-1all
upstream2026.4.0
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-types
??? missing short description for package q2-types :-(
Versions of package q2-types
ReleaseVersionArchitectures
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bookworm2022.11.1-2all
bullseye2020.11.1-1all
upstream2026.4.0
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 License: DFSG free
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2cli
??? missing short description for package q2cli :-(
Versions of package q2cli
ReleaseVersionArchitectures
sid2024.5.0-2all
bookworm2022.11.1-2all
bullseye2020.11.1-1all
upstream2026.4.0
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 License: DFSG free
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Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2templates
??? missing short description for package q2templates :-(
Versions of package q2templates
ReleaseVersionArchitectures
forky2024.5.0+ds-4all
sid2024.5.0+ds-4all
trixie2024.5.0+ds-3all
bullseye2020.11.1+dfsg-1all
bookworm2022.11.1+ds-2all
upstream2026.4.0
Popcon: 2 users (1 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
qiime
??? missing short description for package qiime :-(
Versions of package qiime
ReleaseVersionArchitectures
bullseye2020.11.1-1all
bookworm2022.11.1-2all
sid2024.5.0-1all
upstream2026.4.0
Debtags of package qiime:
roleprogram
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 License: DFSG free
Git
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (PubMed,eprint) Nature Biotechnology 37:852 - 857 (2019)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Topics: Microbial ecology
r-bioc-affxparser
??? missing short description for package r-bioc-affxparser :-(
Versions of package r-bioc-affxparser
ReleaseVersionArchitectures
bookworm1.70.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.78.0-3amd64,arm64,ppc64el,riscv64,s390x
sid1.78.0-4amd64,arm64,loong64,ppc64el,riscv64
upstream1.84.0
Popcon: 1 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
Registry entries: Bio.tools  Bioconda 
r-bioc-affy
??? missing short description for package r-bioc-affy :-(
Versions of package r-bioc-affy
ReleaseVersionArchitectures
sid1.84.0-3amd64,arm64,loong64,ppc64el,riscv64
bookworm1.76.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.84.0-2amd64,arm64,ppc64el,riscv64,s390x
bullseye1.68.0-1amd64,arm64,armhf,i386
upstream1.90.0
Popcon: 136 users (134 upd.)*
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 License: DFSG free
Git
Please cite: Laurent Gautier, Leslie Cope, Benjamin M. Bolstad and Rafael A. Irizarry: affy - analysis of Affymetrix GeneChip data at the probe level. (PubMed,eprint) Bioinformatics (3):307-315 (2004)
Registry entries: Bio.tools  SciCrunch  Bioconda 
r-bioc-affyio
??? missing short description for package r-bioc-affyio :-(
Versions of package r-bioc-affyio
ReleaseVersionArchitectures
bullseye1.60.0-1amd64,arm64,armhf,i386
sid1.76.0-3amd64,arm64,loong64,ppc64el,riscv64
trixie1.76.0-2amd64,arm64,ppc64el,riscv64,s390x
bookworm1.68.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.82.0
Popcon: 137 users (134 upd.)*
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 License: DFSG free
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r-bioc-altcdfenvs
??? missing short description for package r-bioc-altcdfenvs :-(
Versions of package r-bioc-altcdfenvs
ReleaseVersionArchitectures
trixie2.68.0-2all
sid2.68.0-3all
bookworm2.60.0-1all
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upstream2.74.0
Popcon: 1 users (0 upd.)*
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Please cite: Laurent Gautier, Morten Mooller, Lennart Friis-Hansen and Steen Knudsen: Alternative mapping of probes to genes for Affymetrix chips. (PubMed,eprint) BMC Bioinformatics (5):111 (2004)
r-bioc-annotate
??? missing short description for package r-bioc-annotate :-(
Versions of package r-bioc-annotate
ReleaseVersionArchitectures
bullseye1.68.0+dfsg-1all
bookworm1.76.0+dfsg-1all
sid1.84.0+dfsg-3all
trixie1.84.0+dfsg-2all
upstream1.90.0
Popcon: 11 users (37 upd.)*
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r-bioc-annotationdbi
??? missing short description for package r-bioc-annotationdbi :-(
Versions of package r-bioc-annotationdbi
ReleaseVersionArchitectures
sid1.68.0-3all
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bookworm1.60.0-1all
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upstream1.74.0
Popcon: 42 users (38 upd.)*
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r-bioc-annotationhub
??? missing short description for package r-bioc-annotationhub :-(
Versions of package r-bioc-annotationhub
ReleaseVersionArchitectures
bookworm3.6.0+dfsg-1all
sid3.14.0+dfsg-3all
bullseye2.22.0+dfsg-1all
trixie3.14.0+dfsg-2all
upstream4.2.0
Popcon: 32 users (3 upd.)*
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 License: DFSG free
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Registry entries: Bio.tools 
r-bioc-aroma.light
??? missing short description for package r-bioc-aroma.light :-(
Versions of package r-bioc-aroma.light
ReleaseVersionArchitectures
sid3.36.0-3all
bullseye3.20.0-1all
bookworm3.28.0-1all
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upstream3.42.0
Popcon: 8 users (36 upd.)*
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Please cite: Henrik Bengtsson, Pierre Neuvial and Terence P. Speed: TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (PubMed,eprint) BMC Bioinformatics 11:245 (2010)
Registry entries: Bio.tools  SciCrunch  Bioconda 
r-bioc-arrayexpress
??? missing short description for package r-bioc-arrayexpress :-(
Versions of package r-bioc-arrayexpress
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upstream1.72.0
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r-bioc-biocgenerics
??? missing short description for package r-bioc-biocgenerics :-(
Versions of package r-bioc-biocgenerics
ReleaseVersionArchitectures
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trixie0.52.0-2all
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upstream0.58.0
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Please cite: Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K Smyth, Dan Tenenbaum, Levi Waldron and Martin Morgan: Orchestrating high-throughput genomic analysis with Bioconductor. (PubMed) Nature Methods (2015)
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r-bioc-biocneighbors
??? missing short description for package r-bioc-biocneighbors :-(
Versions of package r-bioc-biocneighbors
ReleaseVersionArchitectures
bookworm1.16.0+ds-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.8.2+ds-1amd64,arm64,armhf,i386
sid2.0.1+ds-3amd64,arm64,loong64,ppc64el,riscv64
trixie2.0.1+ds-2amd64,arm64,ppc64el,riscv64,s390x
upstream2.6.0
Popcon: 7 users (37 upd.)*
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 License: DFSG free
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r-bioc-biomart
??? missing short description for package r-bioc-biomart :-(
Versions of package r-bioc-biomart
ReleaseVersionArchitectures
trixie2.62.1+dfsg-1all
bullseye2.46.2+dfsg-1all
bookworm2.54.0+dfsg-1all
sid2.62.1+dfsg-2all
upstream2.68.0
Popcon: 37 users (37 upd.)*
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Please cite: Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. (PubMed) Nature Protocols 4(8):1184-1191 (2009)
Registry entries: Bio.tools 
r-bioc-biomformat
??? missing short description for package r-bioc-biomformat :-(
Versions of package r-bioc-biomformat
ReleaseVersionArchitectures
sid1.34.0+dfsg-3all
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upstream1.40.0
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r-bioc-biostrings
??? missing short description for package r-bioc-biostrings :-(
Versions of package r-bioc-biostrings
ReleaseVersionArchitectures
sid2.74.1+dfsg-3amd64,arm64,loong64,ppc64el,riscv64
bookworm2.66.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.74.1+dfsg-2amd64,arm64,ppc64el,riscv64,s390x
bullseye2.58.0-1amd64,arm64,armhf,i386
upstream2.80.0
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r-bioc-biovizbase
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r-bioc-bitseq
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Please cite: Peter Glaus, Antti Honkela and Magnus Rattray: Identifying differentially expressed transcripts from RNA-seq data with biological variation. (PubMed,eprint) Bioinformatics 28(13):1721–1728 (2012)
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r-bioc-bsgenome
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r-bioc-cner
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r-bioc-complexheatmap
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Please cite: Zuguang Gu, Roland Eils and Matthias Schlesner: Complex heatmaps reveal patterns and correlations in multidimensional genomic data.. (PubMed,eprint) Bioinformatics (2016)
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r-bioc-ctc
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r-bioc-cummerbund
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Please cite: L. Goff and C. Trapnell: cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data (2012)
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r-bioc-dada2
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Please cite: Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson and Susan P Holmes: DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13:581-583 (2016)
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r-bioc-deseq2
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Please cite: Michael I Love, Wolfgang Huber and Simon Anders: Moderated estimation of fold change and dispersion for {RNA}-seq data with {DESeq}2. (eprint) Genome Biol 15(12) (2014)
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r-bioc-dnacopy
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r-bioc-ebseq
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r-bioc-geneplotter
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r-bioc-genomeinfodb
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r-bioc-genomicalignments
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Please cite: Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan and Vincent J. Carey: Software for Computing and Annotating Genomic Ranges. (PubMed,eprint) PLoS Computational Biology 9(8):e1003118 (2013)
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r-bioc-genomicfeatures
??? missing short description for package r-bioc-genomicfeatures :-(
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Please cite: M. Lawrence, W. Huber, H. Pagès, P. Aboyoun and M. Carlson et al.: Software for Computing and Annotating Genomic Ranges. (PubMed,eprint) PLoS Comput Biol 9(8):e1003118 (2013)
r-bioc-genomicranges
??? missing short description for package r-bioc-genomicranges :-(
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r-bioc-geoquery
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Please cite: Sean Davis and Paul Meltzer: GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor Bioinformatics 14,:1846-1847, (2007,)
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r-bioc-go.db
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r-bioc-graph
??? missing short description for package r-bioc-graph :-(
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r-bioc-gseabase
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r-bioc-gsva
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Please cite: Sonja Hänzelmann, Robert Castelo and Justin Guinney: GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics 14(7) (2013)
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r-bioc-gviz
??? missing short description for package r-bioc-gviz :-(
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Please cite: Michael Lawrence, Robert Gentleman and "Vincent Carey: rtracklayer: an R package for interfacing with genome browsers. (PubMed,eprint) Bioinformatics 25(14):1841-1842 (2009)
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r-bioc-hypergraph
??? missing short description for package r-bioc-hypergraph :-(
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r-bioc-impute
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r-bioc-iranges
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r-bioc-limma
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Please cite: Gordon K. Smyth: Limma: linear models for microarray data. (eprint) :397-420 (2005)
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r-bioc-makecdfenv
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r-bioc-mergeomics
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Please cite: Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen and Xia Yang: Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. (eprint) BMC Genomics (2016)
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r-bioc-metagenomeseq
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r-bioc-mofa
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Please cite: Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber and Oliver Stegle: Link to publication Mol Syst Biol 14:e8124 (2018)
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r-bioc-multiassayexperiment
??? missing short description for package r-bioc-multiassayexperiment :-(
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r-bioc-nanostringqcpro
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r-bioc-oligo
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r-bioc-oligoclasses
??? missing short description for package r-bioc-oligoclasses :-(
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r-bioc-org.hs.eg.db
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r-bioc-pcamethods
??? missing short description for package r-bioc-pcamethods :-(
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Please cite: Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther and Joachim Selbig: pcaMethods — a bioconductor package providing PCA methods for incomplete data. (PubMed,eprint) Bioinformatics 23(9):1164–1167 (2007)
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r-bioc-phyloseq
??? missing short description for package r-bioc-phyloseq :-(
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Please cite: Paul J. McMurdie and Susan Holmes: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4):e61217 (2013)
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r-bioc-preprocesscore
??? missing short description for package r-bioc-preprocesscore :-(
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r-bioc-xvector
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Please cite: Thibaut Jombart: adegenet: a R package for the multivariate analysis of genetic markers. (PubMed,eprint) Bioinformatics 24(11):1403-5 (2008)
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r-cran-adephylo
??? missing short description for package r-cran-adephylo :-(
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Please cite: Thibaut Jombart, François Balloux and Stéphane Dray: adephylo: new tools for investigating the phylogenetic signal in biological traits. (PubMed,eprint) Bioinformatics 26(15):1907-1909 (2010)
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r-cran-biwt
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r-cran-dt
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r-cran-fastcluster
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Please cite: Daniel Müllner: fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python. (eprint) Journal of Statistical Software 53(9):1-18 (2013)
r-cran-future.apply
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r-cran-future.batchtools
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r-cran-ica
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r-cran-itertools
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r-cran-kaos
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Please cite: Hannah F. Löchel, Dominic Eger, Theodor Sperlea and Dominik Heider: Deep learning on chaos game representation for proteins. Bioinformatics (2019)
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r-cran-metap
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r-cran-minerva
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r-cran-natserv
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r-cran-nmf
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Please cite: Renaud Gaujoux and Cathal Seoighe: A flexible R package for nonnegative matrix factorization. (PubMed,eprint) BMC Bioinformatics 11(1):367 (2010)
r-cran-optimalcutpoints
??? missing short description for package r-cran-optimalcutpoints :-(
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Please cite: Mónica López-Ratón María Xosé Rodríguez-Álvarez, Carmen Cadarso Suárez and Francisco Gude Sampedro: OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests. Journal of Statistical Software 61(8):1-36 (2014)
r-cran-parmigene
??? missing short description for package r-cran-parmigene :-(
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r-cran-pcapp
??? missing short description for package r-cran-pcapp :-(
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Please cite: V. Todorov and P. Filzmoser: Comparing Classical and Robust Sparse PCA. 190 (2013)
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r-cran-proc
??? missing short description for package r-cran-proc :-(
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r-cran-rann
??? missing short description for package r-cran-rann :-(
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r-cran-rcpphnsw
??? missing short description for package r-cran-rcpphnsw :-(
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r-cran-robustrankaggreg
??? missing short description for package r-cran-robustrankaggreg :-(
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r-cran-rocr
??? missing short description for package r-cran-rocr :-(
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fieldstatistics
roleshared-lib
useanalysing, viewing
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Please cite: Tobias Sing, Oliver Sander, Niko Beerenwinkel and Thomas Lengauer: ROCR: visualizing classifier performance in R. (PubMed,eprint) Bioinformatics 21(20):3940-3941 (2005)
r-cran-rook
??? missing short description for package r-cran-rook :-(
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r-cran-rsvd
??? missing short description for package r-cran-rsvd :-(
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Please cite: N. Benjamin Erichson, Sergey Voronin, Steven L. Brunton and J. Nathan Kutz: Randomized Matrix Decompositions Using R. Journal of Statistical Software 89(11):1-48 (2019)
r-cran-shazam
??? missing short description for package r-cran-shazam :-(
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Please cite: Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari and Steven H. Kleinstein: Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.. (PubMed,eprint) Bioinformatics 31(20):3356-3358 (2015)
Registry entries: Bioconda 
r-cran-sitmo
??? missing short description for package r-cran-sitmo :-(
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r-cran-venndiagram
??? missing short description for package r-cran-venndiagram :-(
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ruby-rgfa
??? missing short description for package ruby-rgfa :-(
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Debian packages in contrib or non-free

python3-seqcluster
??? missing short description for package python3-seqcluster :-(
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Please cite: Lorena Pantano, Marc R. Friedländer, Georgia Escaramís, Esther Lizano, Joan Pallarès-Albanell, Isidre Ferrer, Xavier Estivill and Eulàlia Martí: Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. (PubMed) Bioinformatics (2015)
Registry entries: Bio.tools 
vdjtools
??? missing short description for package vdjtools :-(
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Please cite: M Shugay, D.V. Bagaev, M.A. Turchaninova, D.A. Bolotin, O.V. Britanova, E.V. Putintseva, M.V. Pogorelyy, V.I. Nazarov VI, I.V. Zvyagin, V.I. Kirgizova, K.I. Kirgizov, E.V. Skorobogatova and D.M. Chudakov: VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. (PubMed,eprint) PLoS Comput Biol. 11(11):e1004503 (2015)

Packaging has started and developers might try the packaging code in VCS

libatomicqueue-dev
devel files for C++ atomic_queue library
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C++11 multiple-producer-multiple-consumer lockless queues based on circular buffer with std::atomic. The main design principle these queues follow is simplicity: the bare minimum of atomic operations, fixed size buffer, value semantics.

The circular buffer side-steps the memory reclamation problem inherent in linked-list based queues for the price of fixed buffer size. See Effective memory reclamation for lock-free data structures in C++ for more details.

These qualities are also limitations:

  • The maximum queue size must be set at compile time or construction time.
  • There are no OS-blocking push/pop functions.

Nevertheless, ultra-low-latency applications need just that and nothing more. The simplicity pays off, see the throughput and latency benchmarks.

Available containers are:

  • AtomicQueue - a fixed size ring-buffer for atomic elements.
  • OptimistAtomicQueue - a faster fixed size ring-buffer for atomic elements which busy-waits when empty or full.
  • AtomicQueue2 - a fixed size ring-buffer for non-atomic elements.
  • OptimistAtomicQueue2 - a faster fixed size ring-buffer for non-atomic elements which busy-waits when empty or full.

These containers have corresponding AtomicQueueB, OptimistAtomicQueueB, AtomicQueueB2, OptimistAtomicQueueB2 versions where the buffer size is specified as an argument to the constructor.
libfast-perl
FAST Analysis of Sequences Toolbox
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The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools (for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics modeled after the Unix textutils (such as grep, cut, head, tr, etc). FAST workflows are designed for "inline" (serial) processing of flatfile biological sequence record databases per-sequence, rather than per-line, through Unix command pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm.

You do not need to know Perl or BioPerl to use FAST.
libforester-java
Libraries for evolutionary biology and comparative genomics research
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Forester is a library of Java software for phylogenomics and evolutionary biology research. It can be used to read or write phylogenetic trees, export trees to graphics file,...
libnexml-java
Java API for NeXML
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Java NeXML libraries and tools

  • model: the DOM-based core java 5 NeXML reading/writing API, inside src/main/java as well as JUnit tests inside src/tets/java. The API consists of interfaces in the org.nexml.model package and implementations thereof in the org.nexml.model.impl package.
  • mesquite_module: NeXML import/export functionality for mesquite. This subfolder structure contains classess (inside src/main/java) that depend on the org.nexml.model.* architecture. In addition there are resource files: properties files that map between certain annotation namespaces and/or predicates as encountered in NeXML files, and the Java handler classes that are to be dynamically loaded to operate on them; and a default Tree Style Sheet (TSS) file for marking up tree visualizations.
  • validator: Xerces-J-based XML validator (written by Terri Liebowitz of the San Diego Supercomputing Center, with modifications by Mark Holder) and a ValidateNeXML class that does essentially the same thing, but more tailored to NeXML specifically.
  • transformer: class that transforms NeXML documents into CDAO documents using the xslt stylesheets found in $NEXML_ROOT/xslt.
Please cite: Daniel H. Huson and Celine Scornavacca: Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. (PubMed,eprint) Systematic Biology 61(6):1061–1067 (2012)
python3-compclust
explore and quantify relationships between clustering results
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CompClust is a python package written using the pyMLX and IPlot APIs. It provides software tools to explore and quantify relationships between clustering results. Its development has been largely built around needs of microarray data analysis but could be easily used in other domains.

Briefly pyMLX provides for efficient and convenient execution of many clustering algorithms using a extendable library of algorithms. It also provides many-to-many linkages between data features and annotations (such as cluster labels, gene names, gene ontology information, etc.) These linkages persist through varied data manipulations. IPlot provides an abstraction of the plotting process in which any arbitrary feature or derived feature of the data can be projected onto any feature of the plot, including the X,Y coordinates of points, marker symbol, marker size, maker/line color, etc. These plots are intrinsically linked to the dataset, the View and the Labeling classes found within pyMLX.
python3-consensuscore2
generate consensus sequences for PacBio data -- Python3
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ConsensusCore2 embodies core C++ routines underlying the Arrow HMM algorithm for PacBio multi-sequence consensus. Arrow is the successor to the Quiver model---a CRF model that was embodied in the ConsensusCore C++ library. Compared to Quiver, the Arrow model is more statistically principled and easier and more robust to train.

This package installs the library for Python3.
python3-galaxy-lib
Subset of Galaxy core code base designed to be used
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A small subset of the Galaxy project for reuse outside the core. The Galaxy software framework enables researchers without informatics expertise to perform computational analyses through the web. A user interacts with Galaxy through the web by uploading and analyzing the data. Galaxy interacts with underlying computational infrastructure (servers that run the analyses and disks that store the data) without exposing it to the user.
python3-misopy
Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
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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. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates.

This is the Python 3 module.
Please cite: Yarden Katz, Eric T. Wang, Edoardo M. Airoldi and Christopher B. Burge: Analysis and design of RNA sequencing experiments for identifying isoform regulation. (PubMed) Nature Methods 7(12):1009–1015 (2010)
python3-scanpy
Single-Cell Analysis in Python
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Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
Please cite: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis: SCANPY: large-scale single-cell gene expression data analysis. (eprint) Genome Biology 19(15) (2018)
Registry entries: Bio.tools  SciCrunch  Bioconda 
q2-composition
QIIME2 plugin for Compositional statistics
Versions of package q2-composition
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 License: BSD-3-clause
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QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:

  • Integrated and automatic tracking of data provenance
  • Semantic type system
  • Plugin system for extending microbiome analysis functionality
  • Support for multiple types of user interfaces (e.g. API, command line, graphical)

QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.

QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-deblur
QIIME2 plugin to wrap the Deblur software for sequence quality control
Versions of package q2-deblur
ReleaseVersionArchitectures
VCS2023.9.0-1all
Versions and Archs
 License: BSD-3-clause
Debian package not available
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Version: 2023.9.0-1

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:

  • Integrated and automatic tracking of data provenance
  • Semantic type system
  • Plugin system for extending microbiome analysis functionality
  • Support for multiple types of user interfaces (e.g. API, command line, graphical)

QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.

QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
Please cite: Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez and Rob Knight: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. (PubMed,eprint) mSystems 2 (2017)
q2-diversity
QIIME2 plugin for core diversity analysis
Versions of package q2-diversity
ReleaseVersionArchitectures
VCS2021.8.0-1all
Versions and Archs
 License: BSD-3-clause
Debian package not available
Git
Version: 2021.8.0-1

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. Functionality is made available through QIIME 2 plugins.

This plugin provides the means to statistically assess the diversity of microbiota. This has direct clinical interest, since with whatever we eat or have antibiotics applied, the survival of different groups of bacteria/yeasts will be affected. From these relative abundances of strains that constribute the microbiome, most prominently, comparisons within a group of samples (or an individual) determines the alpha diversity and between (groups of) samples the beta diversity is inspected.

This package is key to most workflows in qiime.
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-gneiss
QIIME2 plugin for Compositional Data Analysis and Visualization
Versions of package q2-gneiss
ReleaseVersionArchitectures
VCS2020.11.1-1all
Versions and Archs
 License: BSD-3-clause
Debian package not available
Git
Version: 2020.11.1-1

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:

  • Integrated and automatic tracking of data provenance
  • Semantic type system
  • Plugin system for extending microbiome analysis functionality
  • Support for multiple types of user interfaces (e.g. API, command line, graphical)

QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.

QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-longitudinal
QIIME2 plugin for longitudinal studies and paired comparisons
Versions of package q2-longitudinal
ReleaseVersionArchitectures
VCS2023.9.1+ds-1all
Versions and Archs
 License: BSD-3-clause
Debian package not available
Git
Version: 2023.9.1+ds-1

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:

  • Integrated and automatic tracking of data provenance
  • Semantic type system
  • Plugin system for extending microbiome analysis functionality
  • Support for multiple types of user interfaces (e.g. API, command line, graphical)

QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.

QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
Please cite: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. (eprint) Nature Biotechnology 37 (2019)
q2-vsearch
QIIME 2 plugin for clustering and dereplicating with vsearch
Versions of package q2-vsearch
ReleaseVersionArchitectures
VCS2023.9.0-1all
Versions and Archs
 License: BSD-3-clause
Debian package not available
Git
Version: 2023.9.0-1

A QIIME 2 plugin that wraps the vsearch application, and provides methods for clustering and dereplicating features and sequences.
Please cite: Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince and Frédéric Mahé: VSEARCH: a versatile open source tool for metagenomics. PeerJ 4 (2016)
r-bioc-bridgedbr
identifier mapping between biological databases
Versions of package r-bioc-bridgedbr
ReleaseVersionArchitectures
VCS2.4.0+dfsg-1all
Versions and Archs
 License: MIT
Debian package not available
Git
Version: 2.4.0+dfsg-1

Use BridgeDb functions and load identifier mapping databases in R.
r-cran-drinsight
drug repurposing on transcriptome sequencing data
Versions of package r-cran-drinsight
ReleaseVersionArchitectures
VCS0.1.1-1all
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 License: GPL-2
Debian package not available
Git
Version: 0.1.1-1

The package's name is an acronym for "Drug Repurposing Integration and Systematic Investigation of Genomic High Throughput Data", which pretty much describes it: This is a connectivity mapping-based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs.
Please cite: Jinyan Chan, Xuan Wang, Jacob A Turner, Nicole E Baldwin and Jinghua Gu: Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. (PubMed,eprint) Bioinformatics 35(16):2818–2826 (2019)
r-other-apmswapp
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
Versions of package r-other-apmswapp
ReleaseVersionArchitectures
VCS1.0-1all
Versions and Archs
 License: <license>
Debian package not available
Git
Version: 1.0-1

The reliable detection of protein-protein-interactions by affinity purification mass spectrometry (AP-MS) is a crucial stepping stone for the understanding of biological processes. The main challenge in a typical AP-MS experiment is to separate true interaction proteins from contaminants by contrasting counts of proteins binding to specific baits with counts of negative controls.
Please cite: Martina Fischer, Susann Zilkenat, Roman G. Gerlach, Samuel Wagner and Bernhard Y. Renard: Pre- and post-processing workflow for affinity purification mass spectrometry data. (PubMed) Journal of Proteome Research 13(5):2239-49 (2014)

No known packages available

bioclipse
platform for chemo- and bioinformatics based on Eclipse
License: Eclipse Public License (EPL) + exception
Debian package not available

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

Bioclipse will provide functionality for chemo- and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin. To stay updated on upcoming features, releases, new plugins etc, please register for the mailing list bioclipse-announce. The development is best followed on the Bioclipse Wiki where we document the progress and ideas of the development on a daily basis.
octace-bioinfo
Bioinformatics manipulation for Octave
License: GPL-2+
Debian package not available 
 aa2int:
   Convert amino acid characters into integers.
 aminolookup:
   Convert between amino acid representations.
 cleave:
   Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern.
 int2aa
   Convert amino acid integers into characters.
 seqreverse
   Reverse a nucleotide sequence.
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 284384