To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("RforProteomics")

In most cases, you don't need to download the package archive at all.

RforProteomics

 

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

Bioconductor version: Release (3.1)

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 descibed 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>

Citation (from within R, enter citation("RforProteomics")):

Installation

To install this package, start R and enter:

source("http://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 R Script Visualisation of proteomics data using R and Bioconductor
PDF   Reference Manual
Text   NEWS

Details

biocViews ExperimentData, MassSpectrometryData
Version 1.6.0
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 (>= 1.11), 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
SystemRequirements
Enhances cleaver
URL http://lgatto.github.com/RforProteomics/
Depends On Me
Imports Me
Suggests Me proteoQC, qcmetrics
Build Report  

Package Archives

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

Package Source RforProteomics_1.6.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Browse/checkout source (username/password: readonly)
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