DebiChem Project
Summary
Analytical biochemistry
DebiChem - analytisk BioChemistry

Denne metapakke vil installere pakker, som gør, at du kan:

  • indlæse og konvertere datafiler for massespektrometri
  • redigere biopolymersekvenser
  • uddybe komplekse arbejdsforløb for massespektrometri
  • udføre proteindatabasesøgninger med brug af tandem-ms-data
  • se og undersøge massespektrometridata

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

Links to other tasks

DebiChem Analytical biochemistry packages

Official Debian packages with high relevance

Libmstoolkit-tools
libraries for manipulating mass spectrometry data - tools
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The MSToolkit is a light-weight C++ library for reading, writing, and manipulating mass spectrometry data. The MSToolkit is easily linked to virtually any C++ algorithm for simple, fast file reading and analysis.

Supported File Formats:

  • read-only mzML including internal compression (zlib and numpress) and external compression (.mzML.gz) read-only;
  • read-only mzXML including internal compression (zlib) and external compression (.mzXML.gz)
  • read/write mgf, ms1, ms2, bms1, bms2, cms1, cms2

Simple Interface:

  • Open any file format from a single function call;
  • Store any spectrum in a simple, comprehensive data structure;
  • Sequential or random-access file reading.

This package ships a MS/MS spectrum loader tool.

Libpwiz-tools
ProteoWizard command line tools
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The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files.

This package ships command line tools that include idconvert (conversion of MS identifications) and msconvert (conversion of MS raw data files from/to any supported format).

Please cite: M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B. Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner, K. Kani, C. Moulding, S.L. Seymour, L.M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E.W. Deutsch, R.L. Moritz, J.E. Katz, D.B. Agus, M. MacCoss, D.L. Tabb and P. Mallick: A cross-platform toolkit for mass spectrometry and proteomics.. (PubMed) Nature Biotechnology 30:918-920 (2012)
Lutefisk
De novo-fortolkning af peptide CID-spektre
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Lutefisk udfører en de novo-fortolkning af kollisionspåførte nedbrydningsspektre (CID), ved at give brugeren en fil indeholdende alle de mulige sekvenskandidater, der svarer til CID-dataene.

Massxpert
polymer chemistry modelling and mass spectrometry data simulation (runtime)
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massXpert allows the user to perform the following tasks:

  • Make brand new polymer chemistry definitions;
  • Use the definitions to easily perform calculations in a desktop calculator-like manner;
  • Perform sophisticated polymer sequence editing and simulations;
  • Perform m/z list comparisons;

Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches...

This package ships the massXpert program.

Registry entries: Bio.tools  OMICtools 
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Mmass
Massespektrometriværktøj for proteomik
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mMass er en fri massespektrum fremviser/analyseprogram hvor de følgende proteomikrelaterede opgaver kan udføres:

  • Åbn rå tekst, mzXML- og mzData-massespektra
  • Definer højdelister
  • Funktionsrig massespektrumsfremviser (zoom, markør ...)
  • Omkalibrering af data
  • Simulationer kun med proteiner
  • Mascot-søgninger på nettet

Programmet kan nemt udvides med yderligere Pythonmoduler. Denne pakke indeholder de platformsuafhængige dele af programmet.

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)
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Openms
Pakke for LC/MS-datahåndtering og -analyse
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OpenMS er en pakke for LC/MS-datahåndtering og -analyse. OpenMS tilbyder en infrastruktur for udvikling af programmer relateret til massespektrometri og funktionsrige 2D- og 3D-virtualiseringsløsninger.

TOPP (OpenMS proteomisk datakanal) er en datakanal for analyse af HPLC/MS-data. Det består af et sæt af utallige små programmer, som kan kædes sammen for at oprette analysedatakanaler skræddersyet for et specifikt problem.

Denne pakke er en metapakke, som afhænger af både bibliotekspakken libopenms (libOpenMS og libOpenMS_GUI) og pakken OpenMS Proteomic Pipeline (topp).

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  OMICtools  Bioconda 
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Python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
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python-pymzml is an extension to Python that offers:

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools;
  • a very fast parser for mzML data, the standard in mass spectrometry data format;
  • a set of functions to compare or handle spectra.

This package contains python-pymzml for Python 3.

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
GNU R-pakke til kvantitativ analyse af massespektrometri data
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MALDIquant tilbyder en komplet analyse pipeline for MALDI-TOF og andre massespektrometriske data. Særlige funktioner omfatter baseline subtraktion ved hjælp af SNIP-algoritme, toppunktstilpasning ved hjælp af warp-funktioner, håndtering af replikerede målinger samt ved at tillade spektre med forskellige opløsninger.

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
GNU R-pakker der tilbyder import/eksport-rutiner for MALDIquant
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MALDIquantForeign-pakken læser (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5) og skriver (tab, csv, msd, mzML) forskellige filformater for massespektrometridata til/fra MALDIquant- objekter.

R-cran-mixtools
GNU R tools for analyzing finite mixture models
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The GNU R mixtools package is a collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

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
GNU R-pakke til at læse Bruker dAltonics *flex-formatfiler
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Pakken readBrukerFlexDAta læser datafilerne indhentet af MALDI-TOF MS på Bruker Daltonics-maskiner i *flex-serien.

R-cran-readmzxmldata
GNU R-pakke til at læse massespektrometridata i mzXML-format
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Pakken readMzXmlData indeholder funktioner for læsning af massespektrometridata i mzXML-formatet.

R-other-amsmercury
Effektiv beregning af nøjagtige masser og mængderne af isotopiske toppe
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Denne GNU R-pakke tilbyder effektiv beregning af nøjagtige masser og mængderne af isotopiske toppe. Det er en forudsætning for R NITPICK, som udfører topidentifikation for massespektrometridata.

R-other-curvefdp
estimation of confidence levels for peptide identifications
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This is a GNU R package for the Analytical Chemistry publication entitled 'Estimating the Confidence of Peptide Identifications without Decoy Databases'. The function curveFDR(scores) fits a gaussian mixture model to a score distribution of peptide identifications and thereby allows the estimation of confidence levels based on the false discvory proportion.

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
Mindste vinkelregression, lasso, positiv lasso og fremad stagewise
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Denne GNU R-pakke indeholder effektive procedurer for montering af en hel lassosekvens med prisen på en enkelt mindste kvadraters-tilpasning. Mindste vinkelregression og infinitessimal fremad stagewise-regression er relateret til lasso beskrevet i http://www- stat.stanford.edu/~hastie/Papers/#LARS.

Dette er en modificeret version af den oprindelige pakke lars ved Hastie og Efron, der tilbyder en LARS-modifikation for ikke-negative lasso.

R-other-nitpick
peak identification for mass spectrometry data
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This R package allows reliable extraction of features from mass spectra and helps in the automated analysis of proteomic mass spectrometry (MS) experiments.

This is the NITPICK implementation for peak picking in MS spectra.

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
Massespektrometriprogram for proteinidentifikation
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X! Tandem kan matche tandem-massespektre med peptidsekvenser, i en proces, der er almindeligt anvendt til at udføre proteinidentifikation.

Dette program har en meget enkel og ukompliceret programmeringsgrænseflade: Det tager simpelthen en XML-fil med instruktioner på sin kommandolinje, og viser resultaterne i en XML-fil, der er specificeret i den anvendte XML-fil. Resultatfilens format er beskrevet på http://www.thegpm.org/docs/X_series_output_form.pdf

I modsætning til nogle tidligere søgemaskiner beregner alle X!-seriens søgemaskiner statistisk tillid (forventningsværdier) for alle de individuelle spektrum-til-sekvens opgaver. De samler også alle peptidopgaverne i et datasæt på de kendte proteinsekvenser og tildeler den statistiske tillid at denne samling og justering ikke er tilfældig. Formlen for dette kan findes her. Derfor er der ikke brug for separate samlings- og statistiske analyseprogrammer, f.eks. PeptideProphet og ProteinProphet.

Official Debian packages with lower relevance

Libpwiz-dev
Bibliotek til at udføre proteomics-dataanalyser - udviklingsfiler
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Biblioteket libpwiz fra projektet ProteoWizard tilbyder et modulopbygget sæt af værktøjer og biblioteker for flere platforme, der kan udvides. Værktøjerne udfører proteomics-dataanalyser; bibliotekerne aktiverer hurtig værktøjsoprettelse ved at tilbyde en robust, klar til tilslutning udviklingsramme, der forenkler og forener datafiladgang, og udfører standardkemi og LCMS-datasætberegninger.

Det primære formål med ProteoWizard er at eliminere de eksisterende barrierer til proteomic-programudvikling, så at forskere kan fokusere på udvikling af nye analytiske fremgangsmåder, frem for at skulle dedikere signifikante ressourcer til hverdagsagtige (hvis vigtige) opgaver, såsom at læse datafiler.

Denne pakke indeholder udviklingsfilerne for biblioteket.

Please cite: M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B. Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner, K. Kani, C. Moulding, S.L. Seymour, L.M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E.W. Deutsch, R.L. Moritz, J.E. Katz, D.B. Agus, M. MacCoss, D.L. Tabb and P. Mallick: A cross-platform toolkit for mass spectrometry and proteomics.. (PubMed) Nature Biotechnology 30:918-920 (2012)

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

Biceps
error-tolerant peptide identification
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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)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 201026