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@ -3383,3 +3383,50 @@ diagnostic plots of fragment size distribution, proportion of mitochondria
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reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
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reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
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footprints.")
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footprints.")
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(license license:gpl2+)))
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(license license:gpl2+)))
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(define-public r-gofuncr
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(package
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(name "r-gofuncr")
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(version "1.2.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "GOfuncR" version))
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(sha256
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(base32
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"021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
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(properties `((upstream-name . "GOfuncR")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-genomicranges" ,r-genomicranges)
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("r-gtools" ,r-gtools)
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("r-iranges" ,r-iranges)
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("r-mapplots" ,r-mapplots)
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("r-rcpp" ,r-rcpp)
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("r-vioplot" ,r-vioplot)))
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(home-page "https://bioconductor.org/packages/GOfuncR/")
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(synopsis "Gene ontology enrichment using FUNC")
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(description
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"GOfuncR performs a gene ontology enrichment analysis based on the
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ontology enrichment software FUNC. GO-annotations are obtained from
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OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
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included in the package and updated regularly. GOfuncR provides the standard
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candidate vs background enrichment analysis using the hypergeometric test, as
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well as three additional tests:
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@enumerate
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@item the Wilcoxon rank-sum test that is used when genes are ranked,
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@item a binomial test that is used when genes are associated with two counts,
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and
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@item a Chi-square or Fisher's exact test that is used in cases when genes are
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associated with four counts.
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@end enumerate
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To correct for multiple testing and interdependency of the tests, family-wise
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error rates are computed based on random permutations of the gene-associated
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variables. GOfuncR also provides tools for exploring the ontology graph and
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the annotations, and options to take gene-length or spatial clustering of
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genes into account. It is also possible to provide custom gene coordinates,
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annotations and ontologies.")
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(license license:gpl2+)))
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