GSVA

Gene Set Variation Analysis for microarray and RNA-seq data

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("GSVA")

Documentation

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

Details

biocViews GeneSetEnrichment, Microarray, Pathways, Software
Version 1.12.0
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 Downloads

Package Source GSVA_1.12.0.tar.gz
Windows Binary GSVA_1.12.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GSVA_1.12.0.tgz
Mac OS X 10.9 (Mavericks)
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