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authorRicardo Wurmus <rekado@elephly.net>2019-03-06 15:55:54 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-06 15:55:54 +0100
commitcb66fb101f392a59dab6f81048abe9356c30361a (patch)
tree6ecdd3b0cb7ba5bcfda4bcc7c58ec52ed1532276 /gnu/packages/bioinformatics.scm
parentafeb10a056e1f5f2c492ace9ee0a33f09cb53e8a (diff)
gnu: Add r-scde.
* gnu/packages/bioinformatics.scm (r-scde): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm42
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4b775d8b7d..196c563625 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6280,6 +6280,48 @@ sequence.")
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
+(define-public r-scde
+ (package
+ (name "r-scde")
+ (version "1.99.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/hms-dbmi/scde.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-mgcv" ,r-mgcv)
+ ("r-rook" ,r-rook)
+ ("r-rjson" ,r-rjson)
+ ("r-cairo" ,r-cairo)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-edger" ,r-edger)
+ ("r-quantreg" ,r-quantreg)
+ ("r-nnet" ,r-nnet)
+ ("r-rmtstat" ,r-rmtstat)
+ ("r-extremes" ,r-extremes)
+ ("r-pcamethods" ,r-pcamethods)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-flexmix" ,r-flexmix)))
+ (home-page "https://hms-dbmi.github.io/scde/")
+ (synopsis "R package for analyzing single-cell RNA-seq data")
+ (description "The SCDE package implements a set of statistical methods for
+analyzing single-cell RNA-seq data. SCDE fits individual error models for
+single-cell RNA-seq measurements. These models can then be used for
+assessment of differential expression between groups of cells, as well as
+other types of analysis. The SCDE package also contains the pagoda framework
+which applies pathway and gene set overdispersion analysis to identify aspects
+of transcriptional heterogeneity among single cells.")
+ ;; See https://github.com/hms-dbmi/scde/issues/38
+ (license license:gpl2)))
+
(define-public r-centipede
(package
(name "r-centipede")