RforProteomics

This is the released version of RforProteomics; for the devel version, see RforProteomics.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

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

Bioconductor version: Release (3.23)

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")):

Laurent Gatto. RforProteomics: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication. doi:10.18129/B9.bioc.RforProteomics, R package version 1.50.0, https://bioconductor.org/packages/RforProteomics.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("RforProteomics")

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

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, MassSpectrometryData, ReproducibleResearch
Version	1.50.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), MSnbase (>= 2.35.2)
Imports	R.utils, biocViews, BiocManager
System Requirements
URL	http://lgatto.github.com/RforProteomics/

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, 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, r-universe

Package Archives

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

Source Package	RforProteomics_1.50.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats