From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: 28029@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#28029] [PATCH 1/2] gnu: Add r-dexseq.
Date: Wed, 9 Aug 2017 19:40:22 +0200 [thread overview]
Message-ID: <20170809174023.23455-1-ricardo.wurmus@mdc-berlin.de> (raw)
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 02b338be6..478a756fb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5791,6 +5791,49 @@ differential expression based on a model using the negative binomial
distribution.")
(license license:lgpl3+)))
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
(define-public r-annotationforge
(package
(name "r-annotationforge")
--
2.13.0
next reply other threads:[~2017-08-09 17:42 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-08-09 17:40 Ricardo Wurmus [this message]
2017-08-09 17:40 ` [bug#28030] [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
2017-08-16 8:51 ` bug#28030: " Ricardo Wurmus
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
2017-08-14 10:03 ` bug#28029: " Ricardo Wurmus
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