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

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npGSEA

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Bioconductor version: Release (2.14)

Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

Author: Jessica Larson and Art Owen

Maintainer: Jessica Larson <larson.jessica at gene.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("npGSEA")

 

PDF R Script Running gene set enrichment analysis with the "npGSEA" package
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, Microarray, Pathways, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends GSEABase(>= 1.24.0)
Imports Biobase, methods, BiocGenerics, graphics, stats
Suggests ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle
System Requirements
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Depends On Me
Imports Me
Suggests Me

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Package Source npGSEA_1.0.0.tar.gz
Windows Binary npGSEA_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) npGSEA_1.0.0.tgz
Mac OS X 10.9 (Mavericks) npGSEA_1.0.0.tgz
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