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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2018-09-24 13:24:13 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-09-24 13:31:20 +0200
commite72702475da2379e10ca09e724e10a9bceceef1b (patch)
tree0e6b2be53208ae75ced5edc1f6e992f4c4021da5
parent28829c040f92399c0705f968f232543e97e5f5f9 (diff)
downloadpatches-e72702475da2379e10ca09e724e10a9bceceef1b.tar
patches-e72702475da2379e10ca09e724e10a9bceceef1b.tar.gz
gnu: Add r-bseqsc.
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm45
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2366843d87..e74abf005f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13824,3 +13824,48 @@ cell-specific differential expression from measured cell proportions using
SAM.")
;; Any version
(license license:lgpl2.1+))))
+
+(define-public r-bseqsc
+ (let ((revision "1")
+ (commit "fef3f3e38dcf3df37103348b5780937982b43b98"))
+ (package
+ (name "r-bseqsc")
+ (version (git-version "1.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/shenorrLab/bseqsc.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-cssam" ,r-cssam)
+ ("r-dplyr" ,r-dplyr)
+ ("r-e1071" ,r-e1071)
+ ("r-edger" ,r-edger)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-nmf" ,r-nmf)
+ ("r-openxlsx" ,r-openxlsx)
+ ("r-pkgmaker" ,r-pkgmaker)
+ ("r-plyr" ,r-plyr)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-rngtools" ,r-rngtools)
+ ("r-scales" ,r-scales)
+ ("r-stringr" ,r-stringr)
+ ("r-xbioc" ,r-xbioc)))
+ (home-page "https://github.com/shenorrLab/bseqsc")
+ (synopsis "Deconvolution of bulk sequencing experiments using single cell data")
+ (description "BSeq-sc is a bioinformatics analysis pipeline that
+leverages single-cell sequencing data to estimate cell type proportion and
+cell type-specific gene expression differences from RNA-seq data from bulk
+tissue samples. This is a companion package to the publication \"A
+single-cell transcriptomic map of the human and mouse pancreas reveals inter-
+and intra-cell population structure.\" Baron et al. Cell Systems (2016)
+@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
+ (license license:gpl2+))))