DebiChem Project
Summary
Analytical Biochemistry
DebiChem Analytical BioChemistry

This metapackage will install packages which enable you to:

  • load and convert mass spectrometric data files;
  • edit biopolymer sequences;
  • elaborate complex mass spectrometry workflows;
  • perform protein database searches using tandem-ms data;
  • visualize and explore mass spectrometric data;
  • simulate isotopic clusters;
  • implement proteomics workflows.
Translate description

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 DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Analytical Biochemistry packages

Official Debian packages with high relevance

comet-ms
??? missing short description for package comet-ms :-(
Versions of package comet-ms
ReleaseVersionArchitectures
bullseye2019015+cleaned1-3amd64,arm64,armhf,i386
sid2019015+cleaned1-4.1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky2019015+cleaned1-4.1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2019015+cleaned1-4.1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm2019015+cleaned1-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream2021010
Popcon: 7 users (32 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Jimmy K. Eng, Tahmina A. Jahan and Michael R. Hoopmann: Comet: an open source tandem mass spectrometry sequence database search tool. (PubMed) Proteomics 13(1) (2012)
freesasa
??? missing short description for package freesasa :-(
Versions of package freesasa
ReleaseVersionArchitectures
sid2.1.2-6amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie2.1.2-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky2.1.2-6amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm2.1.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream2.1.3
Popcon: 0 users (0 upd.)*
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 License: DFSG free
Git
Please cite: Mitternacht, Simon: FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189 (2016)
libmstoolkit-tools
??? missing short description for package libmstoolkit-tools :-(
Versions of package libmstoolkit-tools
ReleaseVersionArchitectures
trixie82-7.2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid82-7.2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye82-7amd64,arm64,armhf,i386
forky82-7.2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm82-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (0 upd.)*
Versions and Archs
 License: DFSG free
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libpwiz-tools
??? missing short description for package libpwiz-tools :-(
Versions of package libpwiz-tools
ReleaseVersionArchitectures
bullseye3.0.18342-4amd64,arm64,armhf,i386
bookworm3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.0.18342-4.2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 3 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
lutefisk
??? missing short description for package lutefisk :-(
Versions of package lutefisk
ReleaseVersionArchitectures
trixie1.0.7+dfsg-7amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid1.0.7+dfsg-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.0.7+dfsg-7amd64,arm64,armhf,i386
bookworm1.0.7+dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.0.7+dfsg-7amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Debtags of package lutefisk:
fieldbiology, chemistry
roleprogram
sciencecalculation
Popcon: 3 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
massxpert
??? missing short description for package massxpert :-(
Versions of package massxpert
ReleaseVersionArchitectures
bullseye6.0.2-1amd64,arm64,armhf,i386
bookworm7.0.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie8.5.0-2all
Debtags of package massxpert:
biologynuceleic-acids, peptidic
fieldbiology, chemistry
interfacex11
roleprogram
uitoolkitqt
useanalysing, simulating
works-withbiological-sequence
works-with-formatxml
x11application
Popcon: 1 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Filippo Rusconi: massXpert 2, a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data. (PubMed,eprint) Bioinformatics 25(20):2741-2742 (2009)
Registry entries: Bio.tools 
Other screenshots of package massxpert
VersionURL
2.0.3-1https://screenshots.debian.net/screenshot/massxpert/2269
 Screenshots of package massxpert
minexpert2
??? missing short description for package minexpert2 :-(
Versions of package minexpert2
ReleaseVersionArchitectures
forky11.4.2-2.1all
sid11.4.2-2.1all
bullseye7.4.1-1amd64,arm64,armhf,i386
bookworm8.6.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie9.6.0-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Popcon: 7 users (31 upd.)*
Versions and Archs
 License: DFSG free
Git
openms
??? missing short description for package openms :-(
Versions of package openms
ReleaseVersionArchitectures
trixie2.6.0+cleaned1-4all
bullseye2.6.0+cleaned1-3all
bookworm2.6.0+cleaned1-3all
sid2.6.0+cleaned1-6all
upstream2.9.1
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
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)
Registry entries: Bio.tools  SciCrunch  Bioconda 
Screenshots of package openms
python3-pymzml
??? missing short description for package python3-pymzml :-(
Versions of package python3-pymzml
ReleaseVersionArchitectures
bookworm2.5.2+repack1-1all
bullseye2.4.7-3all
sid2.5.10+repack1-5all
forky2.5.10+repack1-5all
upstream2.6.0
Popcon: 4 users (3 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler and C. Fufezan: pymzML - Python module for high throughput bioinformatics on mass spectrometry data. (PubMed,eprint) Bioinformatics, UK 28(7):1052-1053 (2012)
r-cran-maldiquant
??? missing short description for package r-cran-maldiquant :-(
Versions of package r-cran-maldiquant
ReleaseVersionArchitectures
bookworm1.22-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.19.3-2amd64,arm64,armhf,i386
trixie1.22.3-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid1.22.3-1armhf,i386,s390x
forky1.22.3-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid1.22.3-2amd64,arm64,loong64,ppc64el,riscv64
Debtags of package r-cran-maldiquant:
biologypeptidic
devellang:r, library
fieldbiology, chemistry, statistics
roledevel-lib
scienceplotting
useanalysing
Popcon: 3 users (2 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Sebastian Gibb and Korbinian Strimmer: MALDIquant: a versatile R package for the analysis of mass spectrometry data. (PubMed,eprint) Bioinformatics 28(17):2270-2271 (2012)
r-cran-maldiquantforeign
??? missing short description for package r-cran-maldiquantforeign :-(
Versions of package r-cran-maldiquantforeign
ReleaseVersionArchitectures
bullseye0.12-2all
bookworm0.13-1all
trixie0.14.1-1all
forky0.14.1-2all
sid0.14.1-2all
Debtags of package r-cran-maldiquantforeign:
devellang:r
fieldbiology, chemistry
useanalysing
Popcon: 3 users (2 upd.)*
Versions and Archs
 License: DFSG free
Git
r-cran-mixtools
??? missing short description for package r-cran-mixtools :-(
Versions of package r-cran-mixtools
ReleaseVersionArchitectures
bullseye1.2.0-1amd64,arm64,armhf,i386
trixie2.0.0.1-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid2.0.0.1-1armhf,i386,s390x
bookworm2.0.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid2.0.0.1-2amd64,arm64,loong64,ppc64el,riscv64
Popcon: 8 users (34 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Tatiana Benaglia, Didier Chauveau, David R. Hunter and Derek Young: mixtools: An R Package for Analyzing Finite Mixture Models. (eprint) Journal of Statistical Software 32(6):1-29 (2009)
r-cran-readbrukerflexdata
??? missing short description for package r-cran-readbrukerflexdata :-(
Versions of package r-cran-readbrukerflexdata
ReleaseVersionArchitectures
forky1.9.3-2all
sid1.9.3-2all
bullseye1.8.5-3all
bookworm1.9.0-1all
trixie1.9.3-1all
Debtags of package r-cran-readbrukerflexdata:
devellang:r, library
fieldbiology, chemistry, statistics
roledevel-lib
useanalysing
Popcon: 3 users (2 upd.)*
Versions and Archs
 License: DFSG free
Git
r-cran-readmzxmldata
??? missing short description for package r-cran-readmzxmldata :-(
Versions of package r-cran-readmzxmldata
ReleaseVersionArchitectures
trixie2.8.3-1all
bullseye2.8.1-4all
bookworm2.8.2-1all
forky2.8.4-1all
sid2.8.4-1all
Debtags of package r-cran-readmzxmldata:
devellang:r
fieldbiology, chemistry
useanalysing
works-with-formatxml
Popcon: 3 users (2 upd.)*
Versions and Archs
 License: DFSG free
Git
r-other-amsmercury
??? missing short description for package r-other-amsmercury :-(
Versions of package r-other-amsmercury
ReleaseVersionArchitectures
sid1.3.0-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.3.0-4amd64,arm64,armhf,i386
bookworm1.3.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.3.0-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.3.0-4amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
Popcon: 2 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
r-other-curvefdp
??? missing short description for package r-other-curvefdp :-(
Versions of package r-other-curvefdp
ReleaseVersionArchitectures
trixie2.0-6all
sid2.0-6all
bullseye2.0-6all
bookworm2.0-6all
Popcon: 2 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Bernhard Y. Renard abd Wiebke Timm, Marc Kirchner, Judith A. J. Steen, Fred A. Hamprecht and Hanno Steen: Estimating the Confidence of Peptide Identifications without Decoy Databases. (eprint) Analytical Chemistry 82(11):4314-4318 (2010)
r-other-iwrlars
??? missing short description for package r-other-iwrlars :-(
Versions of package r-other-iwrlars
ReleaseVersionArchitectures
sid0.9-5-4amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky0.9-5-4amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
trixie0.9-5-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm0.9-5-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.9-5-4amd64,arm64,armhf,i386
Popcon: 2 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
r-other-nitpick
??? missing short description for package r-other-nitpick :-(
Versions of package r-other-nitpick
ReleaseVersionArchitectures
sid2.0-7all
bullseye2.0-7all
bookworm2.0-7all
trixie2.0-7all
forky2.0-7all
Popcon: 2 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith AJ Steen and Fred A Hamprecht: NITPICK: peak identification for mass spectrometry data. (PubMed,eprint) BMC Bioinformatics 9:355 (2008)
tandem-mass
??? missing short description for package tandem-mass :-(
Versions of package tandem-mass
ReleaseVersionArchitectures
sid201702011-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie201702011-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky201702011-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye201702011-1amd64,arm64,armhf,i386
bookworm201702011-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 9 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Peter Bowden, Ron Beavis and John Marshall: Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system.. (PubMed) Journal of proteomics 73(1):103-111 (2009)
toppic
??? missing short description for package toppic :-(
Versions of package toppic
ReleaseVersionArchitectures
trixie1.5.3+dfsg1-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.8.0+repack1-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.8.0+repack1-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye1.3.0+dfsg1-4amd64,arm64,armhf,i386
bookworm1.5.3+dfsg1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.8.1
Popcon: 2 users (0 upd.)*
Newer upstream!
 License: DFSG free
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xtpcpp
??? missing short description for package xtpcpp :-(
Versions of package xtpcpp
ReleaseVersionArchitectures
bullseye0.4.18-1amd64,arm64,armhf,i386
Popcon: 0 users (0 upd.)*
Versions and Archs
 License: DFSG free
Please cite: Olivier Langella, Benoît Valot, Thierry Balliau, Mélisande Blein-Nicolas, Ludovic Bonhomme and Michel Zivy: X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. (PubMed,eprint) Journal of Proteome Research 16(2):494-503 (2017)

Official Debian packages with lower relevance

libisospec++-dev
??? missing short description for package libisospec++-dev :-(
Versions of package libisospec++-dev
ReleaseVersionArchitectures
trixie2.2.1-4.1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid2.3.2-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky2.3.2-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm2.2.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.1.3-1amd64,arm64,armhf,i386
Popcon: 1 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Mateusz K. Łącki, Michał Startek, Dirk Valkenborg and Anna Gambin: IsoSpec: Hyperfast Fine Structure Calculator. (PubMed,eprint) Analytical Chemistry 89(5):3272-3277 (2017)
libpwiz-dev
??? missing short description for package libpwiz-dev :-(
Versions of package libpwiz-dev
ReleaseVersionArchitectures
sid3.0.18342-4.2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.18342-4amd64,arm64,armhf,i386
Debtags of package libpwiz-dev:
devellibrary
roledevel-lib
Popcon: 0 users (1 upd.)*
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 License: DFSG free
Git
libpwizlite-dev
??? missing short description for package libpwizlite-dev :-(
Versions of package libpwizlite-dev
ReleaseVersionArchitectures
bookworm3.0.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky3.0.14-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye3.0.3-1amd64,arm64,armhf,i386
sid3.0.14-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
trixie3.0.8-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Popcon: 0 users (2 upd.)*
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 License: DFSG free
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Packaging has started and developers might try the packaging code in VCS

biceps
error-tolerant peptide identification
Versions of package biceps
ReleaseVersionArchitectures
VCS0.0.201401-1all
Versions and Archs
 License: BSDlike
Debian package not available
Git
Version: 0.0.201401-1

BICEPS is tool for the error-tolerant identification of peptides based on a statistical regularization scheme. It balances possible improvements in peptide-spectrum-matches by allowing substitutions against the increased risk of false positives. BICEPS can identify peptides containing two or more substitutions as occuring e.g. in cross-species searches.
Please cite: Bernhard Y. Renard‡and Buote Xu, Marc Kirchner, Franziska Zickmann‡and Dominic Winter, Simone Korten‡and Norbert W. Brattig‡and Amit Tzur, Fred A. Hamprecht and Hanno Steen: Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS). (PubMed,eprint) Mol Cell Proteomics ;11(7):M111.014167 (2012)
mmass
Mass spectrometry tool for proteomics
Versions of package mmass
ReleaseVersionArchitectures
VCS5.5.0-4all
Versions and Archs
 License: free
Debian package not available
Git
Version: 5.5.0-4

mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

  • Open raw text, mzXML and mzData mass spectra;
  • Define peak lists;
  • Powerful mass spectrum viewer (zoom, cursor...);
  • Data recalibration;
  • Protein-only simulations;
  • Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-independent parts of the software.
Please cite: Martin Strohalm, Daniel Kavan, Petr Novák, Michael Volný and Vladimír Havlíček: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. (PubMed,eprint) Analytical chemistry (ACS) 82(11):4648-4651 (2010)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 283727