To install this package, start R and enter:

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

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

RforProteomics

DOI: 10.18129/B9.bioc.RforProteomics

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

Bioconductor version: Release (3.5)

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>

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

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 1.14.0
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 proteoQC, qcmetrics
Build Report

Package Archives

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

Source Package RforProteomics_1.14.0.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

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