GNU bug report logs - #47156
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

Previous Next

Full log

Message #32 received at 47156 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47156 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/10] gnu: r-edger: Move to (gnu packages bioconductor).
Date: Mon, 15 Mar 2021 14:01:34 +0100

* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4456d13c8..fb0127b7ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1684,6 +1684,34 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-edger
+  (package
+    (name "r-edger")
+    (version "3.32.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "edgeR" version))
+              (sha256
+               (base32
+                "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
+    (properties `((upstream-name . "edgeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-limma" ,r-limma)
+       ("r-locfit" ,r-locfit)
+       ("r-rcpp" ,r-rcpp)
+       ("r-statmod" ,r-statmod))) ;for estimateDisp
+    (home-page "http://bioinf.wehi.edu.au/edgeR")
+    (synopsis "EdgeR does empirical analysis of digital gene expression data")
+    (description "This package can do differential expression analysis of
+RNA-seq expression profiles with biological replication.  It implements a range
+of statistical methodology based on the negative binomial distributions,
+including empirical Bayes estimation, exact tests, generalized linear models
+and quasi-likelihood tests.  It be applied to differential signal analysis of
+other types of genomic data that produce counts, including ChIP-seq, SAGE and
+CAGE.")
+    (license license:gpl2+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff6996011e..dc0d7a2906 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-edger
-  (package
-    (name "r-edger")
-    (version "3.32.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "edgeR" version))
-              (sha256
-               (base32
-                "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
-    (properties `((upstream-name . "edgeR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-limma" ,r-limma)
-       ("r-locfit" ,r-locfit)
-       ("r-rcpp" ,r-rcpp)
-       ("r-statmod" ,r-statmod))) ;for estimateDisp
-    (home-page "http://bioinf.wehi.edu.au/edgeR")
-    (synopsis "EdgeR does empirical analysis of digital gene expression data")
-    (description "This package can do differential expression analysis of
-RNA-seq expression profiles with biological replication.  It implements a range
-of statistical methodology based on the negative binomial distributions,
-including empirical Bayes estimation, exact tests, generalized linear models
-and quasi-likelihood tests.  It be applied to differential signal analysis of
-other types of genomic data that produce counts, including ChIP-seq, SAGE and
-CAGE.")
-    (license license:gpl2+)))
-
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-- 
2.30.1

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.