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03/26: gnu: Add r-edaseq.
From: |
Ricardo Wurmus |
Subject: |
03/26: gnu: Add r-edaseq. |
Date: |
Mon, 22 May 2017 13:03:15 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 296b3c631c2e8cf42f5a0920cd11c424daec9ea4
Author: Ricardo Wurmus <address@hidden>
Date: Wed May 17 16:38:17 2017 +0200
gnu: Add r-edaseq.
* 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 55c076c..21bf2d4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9052,6 +9052,44 @@ 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
- branch master updated (fd3782d -> 9117448), Ricardo Wurmus, 2017/05/22
- 02/26: gnu: Add r-deseq., Ricardo Wurmus, 2017/05/22
- 07/26: gnu: Add ant-bootstrap., Ricardo Wurmus, 2017/05/22
- 12/26: gnu: Add classpath-jamvm-wrappers., Ricardo Wurmus, 2017/05/22
- 06/26: gnu: Add sablevm., Ricardo Wurmus, 2017/05/22
- 03/26: gnu: Add r-edaseq.,
Ricardo Wurmus <=
- 05/26: gnu: Add sablevm-classpath., Ricardo Wurmus, 2017/05/22
- 15/26: gnu: Add jamvm., Ricardo Wurmus, 2017/05/22
- 04/26: gnu: Add jikes., Ricardo Wurmus, 2017/05/22
- 11/26: gnu: Add jamvm-bootstrap., Ricardo Wurmus, 2017/05/22
- 16/26: gnu: Add ecj-javac-on-jamvm-wrapper-final., Ricardo Wurmus, 2017/05/22
- 24/26: gnu: Add ant/java8., Ricardo Wurmus, 2017/05/22
- 23/26: gnu: ant: Move after bootstrap packages., Ricardo Wurmus, 2017/05/22
- 22/26: gnu: ant: Delete bundled jars., Ricardo Wurmus, 2017/05/22
- 18/26: gnu: icedtea-7: Use icedtea-6 for bootstrapping., Ricardo Wurmus, 2017/05/22
- 17/26: gnu: Add icedtea-6., Ricardo Wurmus, 2017/05/22