  This review presents how R, the popular statistical environment and
programming language, can be used in the frame of proteomics data analysis. A
short introduction to R is given, with special emphasis on some of the features
that make R and its add-on packages a premium software for sound and
reproducible data analysis. The reader is also advised on how to find relevant
R software for proteomics. Several use cases are then presented, illustrating
data input/output, quality control, quantitative proteomics and data analysis.
Detailed code and additional links to extensive documentation are available in
the freely available companion package RforProteomics.
