DOI: 10.18129/B9.bioc.RforProteomics  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see RforProteomics.

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

Bioconductor version: 3.17

This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.

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

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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



HTML 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, MassSpectrometryData, ReproducibleResearch
Version 1.38.1
License Artistic-2.0
Depends R (>= 3.5), MSnbase(>= 2.5.3)
Imports R.utils, biocViews, BiocManager
Suggests AnnotationDbi, rpx(>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver
URL http://lgatto.github.com/RforProteomics/
Depends On Me
Imports Me
Suggests Me MSstatsQC
Links To Me
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Source Package RforProteomics_1.38.1.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/RforProteomics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RforProteomics
Package Short Url https://bioconductor.org/packages/RforProteomics/
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