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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 35/50] gnu: r-sva: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:26:07 +0200	[thread overview]
Message-ID: <20210521202622.26591-35-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>

* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a9365a4018..a7b1c63b56 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent
 samples.")
     (license license:artistic2.0)))
 
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-edger" ,r-edger)
+       ("r-genefilter" ,r-genefilter)
+       ("r-mgcv" ,r-mgcv)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-limma" ,r-limma)))
+    (home-page "https://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment.  It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets.  Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))
+
 (define-public r-systempiper
   (package
     (name "r-systempiper")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6120cb6804..2cc41b7e98 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and
 TAB-Seq.")
     (license license:artistic2.0)))
 
-(define-public r-sva
-  (package
-    (name "r-sva")
-    (version "3.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "sva" version))
-       (sha256
-        (base32
-         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-edger" ,r-edger)
-       ("r-genefilter" ,r-genefilter)
-       ("r-mgcv" ,r-mgcv)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-limma" ,r-limma)))
-    (home-page "https://bioconductor.org/packages/sva")
-    (synopsis "Surrogate variable analysis")
-    (description
-     "This package contains functions for removing batch effects and other
-unwanted variation in high-throughput experiment.  It also contains functions
-for identifying and building surrogate variables for high-dimensional data
-sets.  Surrogate variables are covariates constructed directly from
-high-dimensional data like gene expression/RNA sequencing/methylation/brain
-imaging data that can be used in subsequent analyses to adjust for unknown,
-unmodeled, or latent sources of noise.")
-    (license license:artistic2.0)))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
-- 
2.30.1





  parent reply	other threads:[~2021-05-21 20:30 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   ` [bug#48575] [PATCH 18/50] gnu: r-edaseq: " zimoun
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   ` zimoun [this message]
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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