DOI: 10.18129/B9.bioc.GOfuncR    

This is the development version of GOfuncR; for the stable release version, see GOfuncR.

Gene ontology enrichment using FUNC

Bioconductor version: Development (3.8)

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph is included in the package and updated regularly (10-Apr-2018). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. From version 0.99.14 on it is also possible to provide custom annotations and ontologies.

Author: Steffi Grote

Maintainer: Steffi Grote <steffi_grote at eva.mpg.de>

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


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if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("GOfuncR", version = "devel")


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HTML R Script Introduction to GOfuncR
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biocViews GO, GeneSetEnrichment, Software
Version 1.1.3
License GPL (>= 2)
Depends R (>= 3.4), vioplot (>= 0.2)
Imports Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges(>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats
LinkingTo Rcpp
Suggests Homo.sapiens, BiocStyle, knitr, testthat
Depends On Me
Imports Me ABAEnrichment
Suggests Me
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Source Package GOfuncR_1.1.3.tar.gz
Windows Binary GOfuncR_1.1.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GOfuncR_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOfuncR
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Package Short Url http://bioconductor.org/packages/GOfuncR/
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