From 86763fdd70b48df5e4be5f2df6ac4335d9f7abe5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 9 Aug 2017 19:40:22 +0200
Subject: gnu: Add r-dexseq.

* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92c64cffa0..c5a4dcad93 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")
-- 
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