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W4M specifications


Unique identifier OMICS_23162
Name W4M
Alternative name Workflow4Metabolomics
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes




No version available


  • person_outline W4M Team

Publications for Workflow4Metabolomics

W4M citations


Recommended strategies for spectral processing and post processing of 1D 1H NMR data of biofluids with a particular focus on urine

PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] These include: MetaboAnalyst (Xia et al. , ; Xia and Wishart ) for multivariate analysis, metabolite annotation and biological interpretation, MVAPACK for multivariate analysis (Worley and Powers ), Workflow4Metabolomics for multivariate analysis (Giacomoni et al. ), Metassimulo for multivariate analysis (Muncey et al. ), the Human Metabolome Database (HMDB) for metabolite annotation and biologic […]


Navigating freely available software tools for metabolomics analysis

PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] iple software tools into complete analytical workflows. Although it was originally created for genomics analysis, it is being increasingly used as a general bioinformatics workflow management system. Workflow4metabolomics (Giacomoni et al. ) and Galaxy-M (Davidson et al. ) are Galaxy-based workflows for the analysis of metabolomics data. Workflow4metabolomics (Giacomoni et al. ) encompasses analys […]


Herbivore induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata

PLoS One
PMCID: 5333891
PMID: 28253346
DOI: 10.1371/journal.pone.0173315
call_split See protocol

[…] and the mobile phase (0.2% acetic acid in water–acetonitrile) was programmed from 95: 5 to 5: 95 acetonitrile–water (v: v).Mass spectra data were processed by XCMS using the online version of Galaxy-Workflow4metabolomics [], after conversion of raw spectra to mzXML format. Data processing was performed using centWave method for the peak picking, with a maximum deviation of 4 ppm. The signal/noise […]


NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR based metabolomics

PMCID: 5313591
PMID: 28261014
DOI: 10.1007/s11306-017-1178-y

[…] e regarded as either similar or being included in the same case study, can be processed in batch mode, operating directly a Command Line Tool (CLI) or embedded in a workflow management system such as Workflow4Metabolomics (Giacomoni et al. ) or PhenoMeNal VRE App Library (http://portal.phenomenal-h2020.eu/app-library). […]


Non targeted UHPLC MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling

PMCID: 4831991
PMID: 27123000
DOI: 10.1007/s11306-016-1030-9

[…] data analysis techniques applied. A range of tools [e.g. MetaboAnalyst (http://www.metaboanalyst.ca/)], workflows [e.g. Galaxy-M (https://github.com/Viant-Metabolomics/Galaxy-M; Davidson et al. ) and Workflow4Metabolomics (Giacomoni et al. )] and R packages [e.g. mixOmics; http://mixomics.qfab.org] are available to perform data processing. A random selection of 51 papers (10 % of all papers) publi […]


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W4M institution(s)
INRA, UMR 1019, PFEM, Saint Genes Champanelle, France; CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France; INRA, UMR 1331, PF MetaToul-AXIOM, Toxalim, Toulouse, France; INRA, Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Villenave d’Ornon, France; CEA, LIST, Laboratory for Data Analysis and Smart Systems (LADIS), MetaboHUB Paris, Gif-sur-Yvette, France
W4M funding source(s)
Supported by Biogenouest, Lifegrid (Auvergne), and by the IDEALG project [ANR-10-BTBR-04], IFB [ANR-11- INBS-0013] and MetaboHUB [ANR-11-INBS-0010] grants.

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