GNU bug report logs - #54896
[PATCH] gnu: Add r-absseq.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: bug#54896: closed ([PATCH] gnu: Add r-absseq.)
Date: Thu, 14 Apr 2022 11:31:02 +0000

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Your bug report

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

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 54896 <at> debbugs.gnu.org.

-- 
54896: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=54896
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 54896-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-absseq.
Date: Thu, 14 Apr 2022 13:30:03 +0200

Applied, thanks!

-- 
Ricardo

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-absseq.
Date: Tue, 12 Apr 2022 23:57:55 +0200

* gnu/packages/bioconductor.scm (r-absseq): New variable.
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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
   (package
    (name "r-aneufinderdata")
-- 
2.34.0

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