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From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:25:50 +0200	[thread overview]
Message-ID: <20210521202622.26591-18-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>

* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
---
 gnu/packages/bioconductor.scm   | 40 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 40 ---------------------------------
 2 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69ef513bc6..beb662984d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2127,6 +2127,46 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-edaseq
+  (package
+    (name "r-edaseq")
+    (version "2.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "EDASeq" version))
+       (sha256
+        (base32
+         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
+    (properties `((upstream-name . "EDASeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-aroma-light" ,r-aroma-light)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-shortread" ,r-shortread)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/drisso/EDASeq")
+    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+    (description
+     "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data.  Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization.  Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+    (license license:artistic2.0)))
+
 (define-public r-edger
   (package
     (name "r-edger")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2edb501f9b..b0de0d9880 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,46 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-edaseq
-  (package
-    (name "r-edaseq")
-    (version "2.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "EDASeq" version))
-       (sha256
-        (base32
-         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
-    (properties `((upstream-name . "EDASeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-aroma-light" ,r-aroma-light)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-shortread" ,r-shortread)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/drisso/EDASeq")
-    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
-    (description
-     "This package provides support for numerical and graphical summaries of
-RNA-Seq genomic read data.  Provided within-lane normalization procedures to
-adjust for GC-content effect (or other gene-level effects) on read counts:
-loess robust local regression, global-scaling, and full-quantile
-normalization.  Between-lane normalization procedures to adjust for
-distributional differences between lanes (e.g., sequencing depth):
-global-scaling and full-quantile normalization.")
-    (license license:artistic2.0)))
-
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-- 
2.30.1





  parent reply	other threads:[~2021-05-21 20:29 UTC|newest]

Thread overview: 52+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-05-21 20:21 [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 04/50] gnu: r-topgo: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 05/50] gnu: r-bsgenome: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 06/50] gnu: r-msnid: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 07/50] gnu: r-msnbase: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 08/50] gnu: r-samr: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 09/50] gnu: r-impute: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 10/50] gnu: r-seqpattern: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 11/50] gnu: r-go-db: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 12/50] gnu: r-genomation: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 13/50] gnu: r-genomationdata: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 14/50] gnu: r-pcamethods: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 15/50] gnu: r-mzid: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 16/50] gnu: r-aroma-light: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 17/50] gnu: r-deseq: " zimoun
2021-05-21 20:25   ` zimoun [this message]
2021-05-21 20:25   ` [bug#48575] [PATCH 19/50] gnu: r-interactivedisplaybase: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 20/50] gnu: r-annotationhub: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 21/50] gnu: r-fastseg: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 22/50] gnu: r-affy: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 23/50] gnu: r-keggrest: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 24/50] gnu: r-gage: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 25/50] gnu: r-complexheatmap: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 26/50] gnu: r-genomicfiles: " zimoun
2021-05-21 20:25   ` [bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 28/50] gnu: r-organismdbi: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 29/50] gnu: r-affyio: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 30/50] gnu: r-vsn: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 31/50] gnu: r-biovizbase: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 32/50] gnu: r-ensembldb: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 33/50] gnu: r-mzr: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 34/50] gnu: r-protgenerics: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 35/50] gnu: r-sva: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 36/50] gnu: r-motifrg: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 37/50] gnu: r-seqlogo: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 38/50] gnu: r-zlibbioc: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 39/50] gnu: r-rhtslib: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 40/50] gnu: r-bamsignals: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 41/50] gnu: r-rcas: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 43/50] gnu: r-tximport: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 45/50] gnu: r-annotationfilter: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 46/50] gnu: r-rhdf5: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 47/50] gnu: r-chipseq: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 48/50] gnu: r-copyhelper: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 49/50] gnu: r-copywriter: " zimoun
2021-05-21 20:26   ` [bug#48575] [PATCH 50/50] gnu: r-methylkit: " zimoun
2021-05-31 14:07 ` bug#48575: [PATCH 00/50] Move some Bioconductor packages " Ricardo Wurmus

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