From: zimoun <zimon.toutoune@gmail.com>
To: 43400@debbugs.gnu.org
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#43400] [PATCH 05/12] gnu: r-scran: Move to (gnu packages bioconductor).
Date: Mon, 14 Sep 2020 18:07:40 +0200 [thread overview]
Message-ID: <20200914160747.8983-5-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 ---------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e81e9cd726..77de0e2275 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8336,6 +8336,49 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-scran
+ (package
+ (name "r-scran")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scran" version))
+ (sha256
+ (base32
+ "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-bh" ,r-bh)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dqrng" ,r-dqrng)
+ ("r-edger" ,r-edger)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scater" ,r-scater)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-statmod" ,r-statmod)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/scran")
+ (synopsis "Methods for single-cell RNA-Seq data analysis")
+ (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data. Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+ (license license:gpl3)))
+
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ccdc693e08..dcafbb2d21 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10857,49 +10857,6 @@ various analyses of single-cell RNA-seq gene expression data, with a focus on
quality control.")
(license license:gpl2+)))
-(define-public r-scran
- (package
- (name "r-scran")
- (version "1.16.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "scran" version))
- (sha256
- (base32
- "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-bh" ,r-bh)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dqrng" ,r-dqrng)
- ("r-edger" ,r-edger)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scater" ,r-scater)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-statmod" ,r-statmod)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/scran")
- (synopsis "Methods for single-cell RNA-Seq data analysis")
- (description "This package implements a variety of low-level analyses of
-single-cell RNA-seq data. Methods are provided for normalization of
-cell-specific biases, assignment of cell cycle phase, and detection of highly
-variable and significantly correlated genes.")
- (license license:gpl3)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.28.0
next prev parent reply other threads:[~2020-09-14 18:00 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-09-14 16:04 [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 01/12] gnu: r-fourcseq: Move " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 02/12] gnu: r-preprocesscore: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 03/12] gnu: r-rgraphviz: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 04/12] gnu: r-delayedmatrixstats: " zimoun
2020-09-14 16:07 ` zimoun [this message]
2020-09-14 16:07 ` [bug#43400] [PATCH 06/12] gnu: r-scater: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 07/12] gnu: r-singlecellexperiment: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 08/12] gnu: r-beachmat: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 11/12] gnu: r-hitc: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 12/12] gnu: r-fithic: " zimoun
2020-09-14 16:07 ` [bug#43400] [PATCH 10/12] gnu: r-hdf5array: " zimoun
2020-09-14 19:42 ` bug#43400: [PATCH 00/12] Move some BioConductor " Ricardo Wurmus
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