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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 (3.20)

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RforProteomics")

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

Documentation

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

browseVignettes("RforProteomics")
Using R for proteomics data analysis HTML R Script
Visualisation of proteomics data using R and Bioconductor HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, MassSpectrometryData, ReproducibleResearch
Version 1.43.0
License Artistic-2.0
Depends R (>= 3.5), MSnbase(>= 2.5.3)
Imports R.utils, biocViews, BiocManager
System Requirements
URL http://lgatto.github.com/RforProteomics/
See More
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me MSstatsQC
Links To Me
Build Report Build Report

Package Archives

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

Source Package RforProteomics_1.43.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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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