From: Ricardo Wurmus <rekado@elephly.net>
To: 26963@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: bug#26963: [PATCH 3/3] gnu: Add r-edaseq.
Date: Wed, 17 May 2017 16:52:53 +0200 [thread overview]
Message-ID: <20170517145253.28057-3-rekado@elephly.net> (raw)
In-Reply-To: <20170517145253.28057-1-rekado@elephly.net>
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4c37435ad..35f1e77f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9014,6 +9014,44 @@ differential expression based on a model using the negative binomial
distribution.")
(license license:gpl3+)))
+(define-public r-edaseq
+ (package
+ (name "r-edaseq")
+ (version "2.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EDASeq" version))
+ (sha256
+ (base32
+ "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a"))))
+ (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-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq" ,r-deseq)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)))
+ (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 htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package
--
2.12.2
next prev parent reply other threads:[~2017-05-17 14:54 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-05-17 14:39 bug#26963: Add r-edaseq Ricardo Wurmus
2017-05-17 14:52 ` bug#26963: [PATCH 1/3] gnu: Add r-aroma-light Ricardo Wurmus
2017-05-17 14:52 ` bug#26963: [PATCH 2/3] gnu: Add r-deseq Ricardo Wurmus
2017-05-17 14:52 ` Ricardo Wurmus [this message]
2017-05-30 21:06 ` bug#26963: [PATCH 1/3] gnu: Add r-aroma-light Ricardo Wurmus
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