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### GOfuncR: Gene Ontology Enrichment Using FUNC _GOfuncR_ performs a gene ontology enrichment analysis based on the ontology enrichment software [_FUNC_]( It 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 can be used when genes are associated with two counts, e.g. amino acid changes since a common ancestor in two different species, and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts, e.g. non-synonymous or synonymous variants that are fixed between or variable within species. To correct for multiple testing and interdependency of the tests, family-wise error rates (FWER) 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 during testing. GO-annotations and gene-coordinates are obtained from _OrganismDb_ packages ([_Homo.sapiens_]( by default) or _OrgDb_ and _TxDb_ packages. The gene ontology graph (obtained from [geneontology](, release 01-May-2021), is integrated in the package. It is also possible to provide custom gene coordinates, annotations and ontologies. #### Installation A stable release version can be obtained from [_Bioconductor_]( + Installation from Bioconductor ```r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GOfuncR") ``` The developmental (this) version can be obtained from the ['devel' version of Bioconductor]( or directly from GitHub: + Installation from GitHub ```r if (!requireNamespace("devtools", quietly=TRUE)) install.packages("devtools") devtools::install_github("sgrote/GOfuncR") ``` #### Usage See the [vignette]( for an introduction. Also refer to the man-pages for single functions, e.g. ```r library(GOfuncR) ?go_enrich ?get_anno_categories ```