RforProteomics

DOI: 10.18129/B9.bioc.RforProteomics    

This package is for version 3.9 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: 3.9

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], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb]

Maintainer: Laurent Gatto <lg390 at cam.ac.uk>

Installation

To install this package, start R (version "3.6") 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	1.22.0
License	Artistic-2.0
Depends	MSnbase(>= 2.5.3)
Imports	R.utils, shiny, biocViews, BiocManager
LinkingTo
Suggests	AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate
SystemRequirements
Enhances	cleaver
URL	http://lgatto.github.com/RforProteomics/
Depends On Me
Imports Me
Suggests Me	MSstatsQC, proteoQC, qcmetrics
Links To Me
Build Report

Package Archives

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

Source Package	RforProteomics_1.22.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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