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

GSVA

Gene Set Variation Analysis for microarray and RNA-seq data

Bioconductor version: 2.13

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Author: Justin Guinney (with contributions from Robert Castelo)

Maintainer: Justin Guinney <justin.guinney at sagebase.org>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("GSVA")

 

PDF	R Script	Gene Set Variation Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneSetEnrichment, Microarray, Pathways, Software
Version	1.10.3
In Bioconductor since	BioC 2.8 (R-2.13)
License	GPL (>= 2)
Depends	R (>= 2.13.0), methods, GSEABase(>= 1.17.4)
Imports	methods, BiocGenerics, Biobase, GSEABase
Suggests	limma, RColorBrewer, genefilter, mclust, edgeR, GSVAdata
System Requirements
URL	http://www.sagebase.org
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	GSVA_1.10.3.tar.gz
Windows Binary	GSVA_1.10.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GSVA_1.10.3.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats