Difference between revisions of "Software"

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[http://bioconductor.org/packages/release/bioc/html/metaMS.html metaMS] for GC-MS
 
[http://bioconductor.org/packages/release/bioc/html/metaMS.html metaMS] for GC-MS
 
[https://cran.r-project.org/web/packages/MSeasy/index.html MSeasy] for GC-MS
 
  
 
[http://spectconnect.mit.edu SpectConnect] for GC-MS
 
[http://spectconnect.mit.edu SpectConnect] for GC-MS
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[https://cran.r-project.org/web/packages/MetabolAnalyze MetabolAnalyze] for MS and NMR
 
[https://cran.r-project.org/web/packages/MetabolAnalyze MetabolAnalyze] for MS and NMR
 
[https://www.bioconductor.org/packages/release/bioc/html/mQTL.NMR.html mQTL.NMR] for NMR
 
  
 
[https://cran.r-project.org/web/packages/muma/ muma] for MS and NMR
 
[https://cran.r-project.org/web/packages/muma/ muma] for MS and NMR
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=Software tools for metabolite annotation=
 
=Software tools for metabolite annotation=
 
[http://bioconductor.org/packages/release/bioc/html/CAMERA.html CAMERA], Level 4
 
[http://bioconductor.org/packages/release/bioc/html/CAMERA.html CAMERA], Level 4
 
[http://maltese.dbs.aber.ac.uk:8888/hrmet/index.html MZedDB], Level 4
 
  
 
[http://bioconductor.org/packages/release/bioc/html/Rdisop.html Rdisop], Level 4
 
[http://bioconductor.org/packages/release/bioc/html/Rdisop.html Rdisop], Level 4
  
 
[https://bio.informatik.uni-jena.de/software/sirius SIRIUS and CSI Finger ID], Level 4
 
[https://bio.informatik.uni-jena.de/software/sirius SIRIUS and CSI Finger ID], Level 4
 
[http://www.mcisb.org/resources/putmedid.html PUTMEDID-LCMS], Level 3
 
  
 
[http://labpib.fmrp.usp.br/methods/probmetab ProbMetab], Level 3
 
[http://labpib.fmrp.usp.br/methods/probmetab ProbMetab], Level 3
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[http://spin.ccic.ohio-state.edu/index.php/colmar COLMAR], NMR
 
[http://spin.ccic.ohio-state.edu/index.php/colmar COLMAR], NMR
 
[https://msbi.ipb-halle.de/MetFrag/ MetFrag]
 
  
 
[http://www.massbank.jp/Search MassBank]
 
[http://www.massbank.jp/Search MassBank]
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[http://cfmid.wishartlab.com/ CDM-ID]
 
[http://cfmid.wishartlab.com/ CDM-ID]
 
[https://bio.informatik.uni-jena.de/software/sirius/ SIRIUS and CSI:Finger ID]
 
  
 
[http://ms2lda.org MS2LDA]
 
[http://ms2lda.org MS2LDA]

Revision as of 02:08, 11 June 2021

This page contains a list of the most widely used freely available software and tools that are used primarily in metabolomics based on the review article by Spicer et al[1].

Software tools for data preprocessing

XCMS for LC-MS and GC-MS

MetAlign for LC-MS

MS-DIAL for LC-MS

mzMatch for LC-MS

IDEOM for LC-MS

AMDIS for GC-MS

MetaboliteDetector for GC-MS

MeltDB for LC-MS and GC-MS

metaMS for GC-MS

SpectConnect for GC-MS

rNMR for NMR

Software tools for data post-processing

batchCorr for LC-MS

crmn for LC-MS and GC-MS

EigenMS for LC-MS

KMDA for MS

metabomxtr for LC-MS and GC-MS

Metabnorm for NMR

MetabR for LC-MS

MetNorm for LC-MS, GC-MS and NMR

MSPrep for LC-MS

muma for MS and NMR


Software tools for statistical analysis

Ionwinze for LC-MS

MetabolAnalyze for MS and NMR

muma for MS and NMR

ropls for MS and NMR

MetaboAnalyst for LC-MS and NMR


Software tools for metabolite annotation

CAMERA, Level 4

Rdisop, Level 4

SIRIUS and CSI Finger ID, Level 4

ProbMetab, Level 3

MetAssign–mzMatch, Level 3

MetFrag, Level 2a

CFM-ID, Level 2a

FingerID, Level 2a

MAGMa, Level 2a

MyCompoundID, Level 2a

BATMAN, NMR

Bayesil, NMR

MetaboMiner, NMR

SpinAssign, NMR

COLMAR, NMR

MassBank

MetFusion

CDM-ID

MS2LDA

GNPS


Workflows for the analysis of metabolomics data

Galaxy-M for LC-MS

GNPS for LC-MS

MetaboAnalyst 4.0 for LC-MS and NMR

MAVEN for LC-MS

MAIT for LC-MS

MZmine 2 for LC-MS

Workflow4metabolomics for LC-MS, GC-MS and NMR

XCMS Online for LC-MS and GC-MS

References

  1. Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C., "Navigating freely-available software tools for metabolomics analysis", Metabolomics. 2017;13(9):106. doi: 10.1007/s11306-017-1242-7.