npGSEA
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see npGSEA.
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Bioconductor version: 3.9
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("npGSEA")):
Installation
To install this package, start R (version "3.6") 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")| Running gene set enrichment analysis with the "npGSEA" package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, Microarray, Pathways, Software, StatisticalMethod |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | Artistic-2.0 |
| Depends | GSEABase(>= 1.24.0) |
| Imports | Biobase, methods, BiocGenerics, graphics, stats |
| System Requirements | |
| URL |
See More
| Suggests | ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | npGSEA_1.20.0.tar.gz |
| Windows Binary | npGSEA_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | npGSEA_1.20.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |