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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") 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:

Using R for proteomics data analysis HTML R Script
Visualisation of proteomics data using R and Bioconductor HTML R Script
Reference Manual PDF


biocViews ExperimentData, MassSpectrometryData, ReproducibleResearch
Version 1.42.0
License Artistic-2.0
Depends R (>= 3.5), MSnbase(>= 2.5.3)
Imports R.utils, biocViews, BiocManager
System Requirements
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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,, 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
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Suggests Me MSstatsQC
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Follow Installation instructions to use this package in your R session.

Source Package RforProteomics_1.42.0.tar.gz
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