DOI: 10.18129/B9.bioc.RforProteomics    

This is the development version of RforProteomics; for the stable release version, see RforProteomics.

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

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel


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


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biocViews ExperimentData, MassSpectrometryData, ReproducibleResearch
Version 1.33.0
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, isobar, 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
Build Report  

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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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