RforProteomics

DOI: 10.18129/B9.bioc.RforProteomics    

This package is for version 3.12 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: 3.12

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 "4.0") and enter:

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

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")

 

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

Details

biocViews ExperimentData, MassSpectrometryData, ReproducibleResearch
Version 1.28.1
License Artistic-2.0
Depends R (>= 3.5), MSnbase(>= 2.5.3)
Imports R.utils, shiny, biocViews, BiocManager
LinkingTo
Suggests AnnotationDbi, rpx(>= 1.16.1), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, synapter, synapterdata, 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
SystemRequirements
Enhances
URL http://lgatto.github.com/RforProteomics/
Depends On Me
Imports Me
Suggests Me MSstatsQC, qcmetrics
Links To Me
Build Report  

Package Archives

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

Source Package RforProteomics_1.28.1.tar.gz
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/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: