Difference between revisions of "Software"

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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<ref>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.</ref>.
 
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<ref>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.</ref>.
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'''''The links provided below are to resources and tools on websites operated by organizations that are not affiliated with The Metabolomics Society. The Metabolomics Society does not control these websites and is not responsible for their contents, and our inclusion of the links does not imply any endorsement.'''''
  
 
=Software tools for data preprocessing=
 
=Software tools for data preprocessing=
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''"Disclaimer: The links provided here are for informational purposes only. They do not constitute an endorsement or recommendation by the Metabolomics Society. The Metabolomics Society bears no responsibility for the accuracy, timeliness or completeness of information contained on a linked website".''
 
  
  
 
=References=
 
=References=

Latest revision as of 06:02, 26 July 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].

The links provided below are to resources and tools on websites operated by organizations that are not affiliated with The Metabolomics Society. The Metabolomics Society does not control these websites and is not responsible for their contents, and our inclusion of the links does not imply any endorsement.

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

shinyscreen for MS

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.