Software

R packages

• biodb: a library and a development framework for connecting to chemical and biological databases (DOI:10.18129/B9.bioc.biodb)

• biosigner: signature discovery from omics data (DOI:10.18129/B9.bioc.biosigner)

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

• proFIA: preprocessing of FIA-HRMS data (DOI:10.18129/B9.bioc.proFIA)

• ProMetIS: multi-omics phenotyping of the LAT and MX2 knockout mice (https://github.com/IFB-ElixirFr/ProMetIS)

• ptairMS: Pre-processing PTR-TOF-MS Data (DOI:10.18129/B9.bioc.ptairMS)

• ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data (DOI:10.18129/B9.bioc.ropls)

Datasets; MetaboLights repository

• 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.

Galaxy modules; Galaxy toolshed

• 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)

Workflows and histories; Workflow4Metabolomics e-infrastructure

• W4M00001_Sacurine-statistics (DOI:10.15454/1.4811121736910142E12)

• W4M00002_Sacurine-comprehensive (DOI:10.15454/1.481114233733302E12)

• W4M00003_Diaplasma (DOI:10.15454/1.4811165052113186E12)