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Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

Bioconductor version: Release (2.14)

This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' manuscript. The vignette describes the code and data needed to reproduce the examples and figures descibed in the paper as well as functions to download the PXD000001 data files.

Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb]

Maintainer: Laurent Gatto <lg390 at>

To install this package, start R and enter:

Citation (from within R, enter citation("RforProteomics")):




To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script R for Proteomics
PDF R Script RforProteomics Bioc2013 poster
PDF   Reference Manual
Text   NEWS


biocViews ExperimentData, MassSpectrometry, MassSpectrometryData, Proteomics
Version 1.2.0
License Artistic-2.0
Imports R.utils, Biobase, rpx
Suggests mzR, MSnbase, xcms, msdata, isobar, MALDIquant, MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db,, biomaRt, RColorBrewer, ggplot2, reshape2, knitr, biocViews, xtable
System Requirements
Depends On Me
Imports Me
Suggests Me qcmetrics

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source RforProteomics_1.2.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) RforProteomics_1.2.0.tgz
Mac OS X 10.9 (Mavericks) RforProteomics_1.2.0.tgz
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