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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2018-09-24 13:24:13 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-09-24 13:31:20 +0200 |
| commit | e72702475da2379e10ca09e724e10a9bceceef1b (patch) | |
| tree | 0e6b2be53208ae75ced5edc1f6e992f4c4021da5 | |
| parent | 28829c040f92399c0705f968f232543e97e5f5f9 (diff) | |
| download | patches-e72702475da2379e10ca09e724e10a9bceceef1b.tar patches-e72702475da2379e10ca09e724e10a9bceceef1b.tar.gz | |
gnu: Add r-bseqsc.
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
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+)))) |