Software

R packages

proFIA: preprocessing of FIA-HRMS data (DOI:10.18129/B9.bioc.proFIA)
ptairMS: Pre-processing PTR-TOF-MS Data (DOI:10.18129/B9.bioc.ptairMS)
Spec2Xtract: Pre-processing of MS/MS raw spectra (https://github.com/odisce/Spec2Xtract)
DIANMF: processing of SWATH-DIA metabolomics data (https://github.com/odisce/DIANMF)

phenomis: post-processing and univariate analysis of MS data (DOI:10.18129/B9.bioc.phenomis)

ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data (DOI:10.18129/B9.bioc.ropls)
biosigner: signature discovery from omics data (DOI:10.18129/B9.bioc.biosigner)
ProMetIS: multi-omics phenotyping of the LAT and MX2 knockout mice (https://github.com/IFB-ElixirFr/ProMetIS)

mineMS2: Annotation of spectral libraries with exact fragmentation patterns (https://github.com/odisce/mineMS2)
biodb: a library and a development framework for connecting to chemical and biological databases (DOI:10.18129/B9.bioc.biodb)

MTBLS1903: ProMetIS: deep phenotyping of knock-out mice by proteomics and metabolomics.
MTBLS404: Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses (‘Sacurine’ data set).
MTBLS148: Impact of collection conditions on the metabolite content of human urine samples as analyzed by liquid chromatography coupled to mass spectrometry and nuclear magnetic resonance spectroscopy.

Batch Correction (in collaboration with Jean-Francois Martin, Melanie Petera, Marion Landi and Franck Giacomoni)
Biosigner
Heatmap
Multivariate
proFIA
Quality Metrics (in collaboration with Melanie Petera)
Univariate (in collaboration with Marie Tremblay-Franco)