RforProteomics

DOI: 10.18129/B9.bioc.RforProteomics    

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

Bioconductor version: Release (3.7)

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>

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("http://bioc.ism.ac.jp/biocLite.R")
biocLite("RforProteomics")

Documentation

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

browseVignettes("RforProteomics")

 

HTML R Script Visualisation of proteomics data using R and Bioconductor
HTML R Script Visualisation of proteomics data using R and Bioconductor
PDF   Reference Manual
Text   NEWS

Details

biocViews ExperimentData, MassSpectrometryData, ReproducibleResearch
Version 1.18.1
License Artistic-2.0
Depends MSnbase(>= 2.5.3)
Imports R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, DT, AnnotationDbi, shiny
LinkingTo
Suggests 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
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_1.18.1.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 http://bioconductor.org/packages/RforProteomics/
Package Downloads Report Download Stats

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