To install this package, start R and enter:


In most cases, you don't need to download the package archive at all.


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

Bioconductor version: 3.0

This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' paper. Two vignettes describe the code and data needed to reproduce the examples and figures descibed in the paper and functionality for proteomics visualisation.

Author: Laurent Gatto [aut, cre], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb]

Maintainer: Laurent Gatto <lg390 at>

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


To install this package, start R and enter:



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



PDF R Script A current perspective on using R and Bioconductor for proteomics data analysis
PDF R Script RforProteomics Bioc2013 poster
PDF R Script Using R for proteomics data analysis
HTML R Script Visualisation of proteomics data using R and Bioconductor
PDF   Reference Manual
Text   NEWS


biocViews ExperimentData, MassSpectrometry, MassSpectrometryData, Proteomics
Version 1.4.1
License Artistic-2.0
Depends MSnbase
Imports R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny
Suggests mzR, xcms, msdata, isobar, MALDIquant (>= 1.11), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db,, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, knitr, BiocStyle, MSGFplus, MSGFgui, MSnID
Enhances cleaver
Depends On Me
Imports Me
Suggests Me proteoQC, qcmetrics
Build Report  

Package Archives

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

Package Source RforProteomics_1.4.1.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) RforProteomics_1.4.1.tgz
Mac OS X 10.9 (Mavericks) RforProteomics_1.4.1.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center