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## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("npGSEA")
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Bioconductor version: 3.2
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>
Citation (from within R,
enter citation("npGSEA")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("npGSEA")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("npGSEA")
Running gene set enrichment analysis with the "npGSEA" package | ||
Reference Manual | ||
Text | NEWS |
biocViews | GeneSetEnrichment, Microarray, Pathways, Software, StatisticalMethod |
Version | 1.6.0 |
In Bioconductor since | BioC 2.14 (R-3.1) (2 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 |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | EnrichmentBrowser |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | npGSEA_1.6.0.tar.gz |
Windows Binary | npGSEA_1.6.0.zip |
Mac OS X 10.6 (Snow Leopard) | npGSEA_1.6.0.tgz |
Mac OS X 10.9 (Mavericks) | npGSEA_1.6.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/npGSEA/tree/release-3.2 |
Package Short Url | http://bioconductor.org/packages/npGSEA/ |
Package Downloads Report | Download Stats |
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