Package: GOfuncR Type: Package Title: Gene ontology enrichment using FUNC Version: 1.33.0 Date: 2024-02-03 Author: Steffi Grote Maintainer: Steffi Grote Description: 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. License: GPL (>= 2) Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, Depends: R (>= 3.4), vioplot (>= 0.2), LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat VignetteBuilder: knitr biocViews: GeneSetEnrichment, GO NeedsCompilation: yes Packaged: 2026-06-18 11:26:10 UTC; root Config/pak/sysreqs: libpng-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:47:01 UTC RemoteUrl: https://github.com/bioc/GOfuncR RemoteRef: HEAD RemoteSha: a00a06fdf0baefafc4ab4115dd73497c8c9c2845