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[bug#54896] gnu: Add r-absseq.

Message ID 20220412215755.8819-1-madalinionel.patrascu@mdc-berlin.de
State New
Headers show
Series [bug#54896] gnu: Add r-absseq. | expand


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Commit Message

Mădălin Ionel Patrașcu April 12, 2022, 9:57 p.m. UTC
* gnu/packages/bioconductor.scm (r-absseq): New variable.
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)


Ricardo Wurmus April 14, 2022, 11:30 a.m. UTC | #1
Applied, thanks!
diff mbox series


diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 803437a033..25e02bebad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1139,6 +1139,35 @@  (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (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 @code{ABSSeq} 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
    (name "r-aneufinderdata")