gnu: Add r-gofuncr.

* gnu/packages/bioconductor.scm (r-gofuncr): New variable.
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Ricardo Wurmus 2019-03-29 17:43:52 +01:00
parent 692bce1595
commit 3972cfce6a
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@ -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+)))