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authorRicardo Wurmus <rekado@elephly.net>2019-08-15 17:39:11 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-08-15 17:44:25 +0200
commitbb88417fb70f8881d46e2f2e8235a1aa16591a36 (patch)
treeaecf52e8076a5a932fe99ba64ed79c0c75cef225
parent19f1aac0e7405b99c96823dda36e5389f18f64ec (diff)
downloadpatches-bb88417fb70f8881d46e2f2e8235a1aa16591a36.tar
patches-bb88417fb70f8881d46e2f2e8235a1aa16591a36.tar.gz
gnu: Add r-rcistarget.
* gnu/packages/bioconductor.scm (r-rcistarget): New variable.
-rw-r--r--gnu/packages/bioconductor.scm35
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74620a2cbe..0a0aee7309 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5089,6 +5089,41 @@ by a sparse number of variables, this method can reduce the complexity of
data, to only emphasize the data that actually matters.")
(license license:expat)))
+(define-public r-rcistarget
+ (package
+ (name "r-rcistarget")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RcisTarget" version))
+ (sha256
+ (base32
+ "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
+ (properties `((upstream-name . "RcisTarget")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-aucell" ,r-aucell)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-feather" ,r-feather)
+ ("r-gseabase" ,r-gseabase)
+ ("r-r-utils" ,r-r-utils)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://aertslab.org/#scenic")
+ (synopsis "Identify transcription factor binding motifs enriched on a gene list")
+ (description
+ "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
+over-represented on a gene list. In a first step, RcisTarget selects DNA
+motifs that are significantly over-represented in the surroundings of the
+@dfn{transcription start site} (TSS) of the genes in the gene-set. This is
+achieved by using a database that contains genome-wide cross-species rankings
+for each motif. The motifs that are then annotated to TFs and those that have
+a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
+each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
+genes in the gene-set that are ranked above the leading edge).")
+ (license license:gpl3)))
+
(define-public r-cicero
(package
(name "r-cicero")