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| -rw-r--r-- | gnu/packages/bioconductor.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c0f0520ce8..fb7e5a95f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3383,3 +3383,50 @@ diagnostic plots of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.") (license license:gpl2+))) + +(define-public r-gofuncr + (package + (name "r-gofuncr") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOfuncR" version)) + (sha256 + (base32 + "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk")))) + (properties `((upstream-name . "GOfuncR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-mapplots" ,r-mapplots) + ("r-rcpp" ,r-rcpp) + ("r-vioplot" ,r-vioplot))) + (home-page "https://bioconductor.org/packages/GOfuncR/") + (synopsis "Gene ontology enrichment using FUNC") + (description + "GOfuncR performs a gene ontology enrichment analysis based on the +ontology enrichment software FUNC. GO-annotations are obtained from +OrganismDb or OrgDb packages (@code{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: + +@enumerate +@item the Wilcoxon rank-sum test that is used when genes are ranked, +@item a binomial test that is used when genes are associated with two counts, + and +@item a Chi-square or Fisher's exact test that is used in cases when genes are +associated with four counts. +@end enumerate + +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 license:gpl2+))) |