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authorRoel Janssen <roel@gnu.org>2020-04-26 21:24:03 +0200
committerRoel Janssen <roel@gnu.org>2020-04-26 21:24:03 +0200
commit886125d791bd1e0ca9d28f7adbb74ffb6f662a33 (patch)
tree369b11a2573df75b434fb975520169e42100397d /gnu/packages
parent3699bcf54ac51c99c2807afd60d1eeebc00329ec (diff)
gnu: Add r-motifbreakr.
* gnu/packages/bioconductor.scm (r-motifbreakr): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm48
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9ecf42e783..a27845581f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4022,6 +4022,54 @@ distributions, modules and filter motifs.")
frequency matrices from nine public sources, for multiple organisms.")
(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
(package
(name "r-motifstack")