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gnu: Add r-motifbreakr.

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* gnu/packages/bioconductor.scm (r-motifbreakr): New variable.
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Roel Janssen 2020-04-26 21:24:03 +02:00
parent 3699bcf54a
commit 886125d791
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gnu/packages/bioconductor.scm
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@ -4022,6 +4022,54 @@ (define-public r-motifdb
frequency matrices from nine public sources, for multiple organisms.") frequency matrices from nine public sources, for multiple organisms.")
(license license:artistic2.0))) (license license:artistic2.0)))
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
(version "2.0.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
(base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
`(("r-grimport" ,r-grimport)
("r-stringr" ,r-stringr)
("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-variantannotation" ,r-variantannotation)
("r-biocparallel" ,r-biocparallel)
("r-motifstack" ,r-motifstack)
("r-gviz" ,r-gviz)
("r-matrixstats" ,r-matrixstats)
("r-tfmpvalue" ,r-tfmpvalue)
("r-motifdb" ,r-motifdb)))
(home-page "https://www.bioconductor.org/packages/motifbreakR/")
(synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
(description "This package allows biologists to judge in the first place
whether the sequence surrounding the polymorphism is a good match, and in
the second place how much information is gained or lost in one allele of
the polymorphism relative to another. This package gives a choice of
algorithms for interrogation of genomes with motifs from public sources:
@enumerate
@item a weighted-sum probability matrix;
@item log-probabilities;
@item weighted by relative entropy.
@end enumerate
This package can predict effects for novel or previously described variants in
public databases, making it suitable for tasks beyond the scope of its original
design. Lastly, it can be used to interrogate any genome curated within
Bioconductor.")
(license license:gpl2+)))
(define-public r-motifstack (define-public r-motifstack
(package (package
(name "r-motifstack") (name "r-motifstack")