Guix

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. GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests:

1. the Wilcoxon rank-sum test that is used when genes are ranked,

2. a binomial test that is used when genes are associated with two counts, and

3. 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.