To install this package, start R and enter:

## try http if https is not available
source("https://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:

## try http if https is not available
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	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)
Subversion source	(username/password: readonly)
Package Short Url	http://bioconductor.org/packages/RforProteomics/
Package Downloads Report	Download Stats

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