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authorMădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>2022-04-12 23:57:55 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-04-14 13:29:48 +0200
commitcab66570947a8d6fc1acd380151e91a65cf4a6bb (patch)
treed2aab1b2883a32f08a11919cdede4ec6a68f2974 /gnu/packages/bioconductor.scm
parenta436582124a4e4d1e075bb8ba5eb6a18fbfd8145 (diff)
downloadguix-cab66570947a8d6fc1acd380151e91a65cf4a6bb.tar.gz
gnu: Add r-absseq.
* gnu/packages/bioconductor.scm (r-absseq): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm29
1 files changed, 29 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69ffdbe79b..e6f462b697 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1128,6 +1128,35 @@ raw data, processed data, graphics output and statistical results are organized
 into folders according to the analysis settings used.")
     (license license:gpl2+)))
 
+(define-public r-absseq
+  (package
+    (name "r-absseq")
+    (version "1.48.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ABSSeq" version))
+              (sha256
+               (base32
+                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
+    (properties `((upstream-name . "ABSSeq")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-limma r-locfit))
+    (home-page "https://bioconductor.org/packages/ABSSeq")
+    (synopsis
+     "RNA-Seq analysis based on modelling absolute expression differences")
+    (description
+     "This package implements a new RNA-Seq analysis method and integrates two
+modules: a basic model for pairwise comparison and a linear model for complex
+design.  RNA-Seq quantifies gene expression with reads count, which usually
+consists of conditions (or treatments) and several replicates for each
+condition.  This software infers differential expression directly by the
+counts difference between conditions.  It assumes that the sum counts
+difference between conditions follow a negative binomial distribution.  In
+addition, @code{ABSSeq} moderates the fold-changes by two steps: the
+expression level and gene-specific dispersion, that might facilitate the gene
+ranking by fold-change and visualization.")
+    (license license:gpl3+)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")