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[bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconduc
From: |
zimoun |
Subject: |
[bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor). |
Date: |
Mon, 8 Mar 2021 18:57:56 +0100 |
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 45 ---------------------------------
2 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f2dd4bb70b..883b6df2fb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1525,6 +1525,51 @@ differential expression based on a model using the
negative binomial
distribution.")
(license license:lgpl3+)))
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64585127e6..4fa4a1e354 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,51 +7385,6 @@ includes software to
")
(license license:cc0))))
-(define-public r-dexseq
- (package
- (name "r-dexseq")
- (version "1.36.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DEXSeq" version))
- (sha256
- (base32
- "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
- (properties `((upstream-name . "DEXSeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biomart" ,r-biomart)
- ("r-deseq2" ,r-deseq2)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-statmod" ,r-statmod)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/DEXSeq")
- (synopsis "Inference of differential exon usage in RNA-Seq")
- (description
- "This package is focused on finding differential exon usage using RNA-seq
-exon counts between samples with different experimental designs. It provides
-functions that allows the user to make the necessary statistical tests based
-on a model that uses the negative binomial distribution to estimate the
-variance between biological replicates and generalized linear models for
-testing. The package also provides functions for the visualization and
-exploration of the results.")
- (license license:gpl3+)))
-
(define-public r-annotationforge
(package
(name "r-annotationforge")
--
2.30.1
- [bug#47010] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 05/10] gnu: r-rbgl: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 06/10] gnu: r-gseabase: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 09/10] gnu: r-shortread: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 04/10] gnu: r-annotationforge: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor).,
zimoun <=
- [bug#47010] [PATCH 02/10] gnu: r-deseq2: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 07/10] gnu: r-category: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 08/10] gnu: r-gostats: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- [bug#47010] [PATCH 10/10] gnu: r-systempiper: Move to (gnu packages bioconductor)., zimoun, 2021/03/08
- bug#47010: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor)., Ricardo Wurmus, 2021/03/12