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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[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 | ||
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[http://spectconnect.mit.edu SpectConnect] for GC-MS | [http://spectconnect.mit.edu SpectConnect] for GC-MS | ||
[http://rnmr.nmrfam.wisc.edu rNMR] for NMR | [http://rnmr.nmrfam.wisc.edu rNMR] for NMR | ||
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+ | [https://git-r3lab.uni.lu/eci/shinyscreen shinyscreen] for MS | ||
=Software tools for data post-processing= | =Software tools for data post-processing= | ||
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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 | ||
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[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 | ||
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[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 | ||
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[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 | ||
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[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] | ||
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[http://ms2lda.org MS2LDA] | [http://ms2lda.org MS2LDA] | ||
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[https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage XCMS Online] for LC-MS and GC-MS | [https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage XCMS Online] for LC-MS and GC-MS | ||
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=References= | =References= |
Latest revision as of 07:02, 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.
Contents
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
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
- ↑ 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.