RforProteomics

DOI: 10.18129/B9.bioc.RforProteomics    

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

Bioconductor version: Release (3.6)

This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' paper. Two vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation.

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RforProteomics")

Documentation

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

browseVignettes("RforProteomics")

 

PDF	R Script	A current perspective on using R and Bioconductor for proteomics data analysis
PDF	R Script	RforProteomics Bioc2013 poster
PDF	R Script	Using R for proteomics data analysis
HTML		Visualisation of proteomics data using R and Bioconductor
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, MassSpectrometryData, ReproducibleResearch
Version	1.15.0
License	Artistic-2.0
Depends	MSnbase
Imports	R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, corrplot, Heatplus, gplots, VennDiagram, genefilter
SystemRequirements
Enhances	cleaver
URL	http://lgatto.github.com/RforProteomics/
Depends On Me
Imports Me
Suggests Me	MSstatsQC, proteoQC, qcmetrics
Build Report

Package Archives

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

Source Package	RforProteomics_1.15.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/RforProteomics
Package Short Url	http://bioconductor.org/packages/RforProteomics/
Package Downloads Report	Download Stats