npGSEA

DOI: 10.18129/B9.bioc.npGSEA  

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

Bioconductor version: Release (3.16)

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.jess at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("npGSEA")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.34.0
In Bioconductor since	BioC 2.14 (R-3.1) (9 years)
License	Artistic-2.0
Depends	GSEABase(>= 1.24.0)
Imports	Biobase, methods, BiocGenerics, graphics, stats
LinkingTo
Suggests	ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle
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Package Archives

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

Source Package	npGSEA_1.34.0.tar.gz
Windows Binary	npGSEA_1.34.0.zip
macOS Binary (x86_64)	npGSEA_1.34.0.tgz
macOS Binary (arm64)	npGSEA_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/npGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/npGSEA
Bioc Package Browser	https://code.bioconductor.org/browse/npGSEA/
Package Short Url	https://bioconductor.org/packages/npGSEA/
Package Downloads Report	Download Stats