DOI: 10.18129/B9.bioc.GOfuncR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GOfuncR.

Gene ontology enrichment using FUNC

Bioconductor version: 3.16

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 (01-May-2021). 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. It is also possible to provide custom gene coordinates, annotations and ontologies.

Author: Steffi Grote

Maintainer: Steffi Grote <grote.steffi at gmail.com>

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biocViews GO, GeneSetEnrichment, Software
Version 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (5 years)
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
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Suggests Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
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Source Package GOfuncR_1.18.0.tar.gz
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