GSVA

Gene Set Variation Analysis

Bioconductor version: 2.8

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. Users on all platforms must install the GNU Scientific Library; see the README file, available in the source distribution of this file, for details.

Author: Justin Guinney <justin.guinney at sagebase.org> (with contributions from Robert Castelo <robert.castelo at upf.edu> and Sonja Haenzelmann

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

Details

biocViews Bioinformatics, Microarray, Pathways
Depends R (>= 2.13.0), methods
Imports methods, Biobase, GSEABase
Suggests limma, qpgraph, graph, Rgraphviz, RColorBrewer, genefilter, GSVAdata
System Requirements GNU Scientific Library >= 1.12
License GPL (>= 2)
URL http://www.sagebase.org
Depends On Me
Imports Me
Suggests Me
Version 1.0.1
Since Bioconductor 2.8 (R-2.13)

Package Downloads

Package Source GSVA_1.0.1.tar.gz
Windows Binary GSVA_1.0.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GSVA_1.0.1.tgz
Package Downloads Report Download Stats

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