Proteomics Data Analysis

About

R scripts for quantitative proteomics data analysis, including data normalisation, statistical testing, and visualisation of protein expression profiles. Developed as part of cross-disciplinary bioinformatics support at CR2TI, UMR 1064, Nantes Université.

Prerequisites and genome version

Genome version and annotation :

• Orthologs of Xenopus laevis 9.2 from Xenbase
• SampleAnnot file to describe samples
• SamplePerCond.tsv file that contains all samples to project for a comparison

Key analyses

• Data normalisation and quality control
• Differential protein expression analysis
• Visualisation of normalised data matrices (heatmaps, volcano plots)

Tools

• R / RStudio
• ggplot2, pheatmap, limma

Author

Valentin FRANCOIS--CAMPION — GitHub