The Workflow4Metabolomics, W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
LC/MS and GC/MS Data Analysis
Bioconductor version: Release (3.2)
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Author: Colin A. Smith , Ralf Tautenhahn , Steffen Neumann , Paul Benton , Christopher Conley , Johannes Rainer <Johannes.Rainer at eurac.edu>
Maintainer: Steffen Neumann
Citation (from within R, enter citation("xcms")):
Smith, C.A., Want, E.J., O'Maille, G., Abagyan,R., Siuzdak and G. (2006). “XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification.” Analytical Chemistry, 78, pp. 779–787.
Tautenhahn R, Boettcher C and Neumann S (2008). “Highly sensitive feature detection for high resolution LC/MS.” BMC Bioinformatics, 9, pp. 504.
Benton HP, Want EJ and Ebbels TMD (2010). “Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data.” BIOINFORMATICS, 26, pp. 2488.
Homepage: https://bioconductor.org/packages/release/bioc/html/xcms.html
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Homepage: https://galaxyproject.org/
Conda is package manager that among many other things can be used to manage Python packages.
#To install miniconda2
#http://conda.pydata.org/miniconda.html
#To install the xcms R library using conda:
conda install r-snow bioconductor-xcms r-batch
#To set an environment:
conda create -n bioconductor-xcms r-snow bioconductor-xcms r-batch`
#To activate the environment:
. activate bioconductor-xcms
See: Job Dynamic Destination Mapping for xcmsSet
Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes!
Planemo test using conda: passed
Planemo test using source env.sh: passed
Planemo shed_test: passed
- Gildas Le Corguillé @lecorguille - ABiMS / IFB - UPMC/CNRS - Station Biologique de Roscoff - France
- Misharl Monsoor @mmonsoor - ABiMS / IFB - CNRS/UPMC - Station Biologique de Roscoff - France
- Yann Guitton @yguitton - LABERCA - Laboratory of Food Contaminants and Residue Analysis - Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique - France
- Urszula Czerwinska ABiMS / IFB - CNRS/UPMC - Station Biologique de Roscoff - France
- Pierre Pericard - ABiMS / IFB - CNRS/UPMC - Station Biologique de Roscoff - France