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02/03: gnu: Add r-rcistarget.
From: |
guix-commits |
Subject: |
02/03: gnu: Add r-rcistarget. |
Date: |
Thu, 15 Aug 2019 11:45:22 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit bb88417fb70f8881d46e2f2e8235a1aa16591a36
Author: Ricardo Wurmus <address@hidden>
Date: Thu Aug 15 17:39:11 2019 +0200
gnu: Add r-rcistarget.
* gnu/packages/bioconductor.scm (r-rcistarget): New variable.
---
gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74620a2..0a0aee7 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")