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authorRicardo Wurmus <rekado@elephly.net>2019-07-30 15:52:48 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-07-30 15:52:48 +0200
commitb2dce6b5a2eecb9e20e5ee03779c020b2644666b (patch)
treea5ecd92a2f47d35873cf7180540347185e195a91
parent86c46d712012a55e409770330146117ce05d86c1 (diff)
gnu: Add r-monocle3.
* gnu/packages/bioconductor.scm (r-monocle3): New variable.
-rw-r--r--gnu/packages/bioconductor.scm63
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 98a2da21c9..1adf47b08f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22,6 +22,7 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages base)
@@ -2263,6 +2264,68 @@ tasks on single cell expression data. It is designed to work with RNA-Seq and
qPCR data, but could be used with other types as well.")
(license license:artistic2.0)))
+(define-public r-monocle3
+ (package
+ (name "r-monocle3")
+ (version "0.1.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cole-trapnell-lab/monocle3.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-grr" ,r-grr)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-limma" ,r-limma)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-matrix-utils" ,r-matrix-utils)
+ ("r-pbapply" ,r-pbapply)
+ ("r-pbmcapply" ,r-pbmcapply)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plotly" ,r-plotly)
+ ("r-pryr" ,r-pryr)
+ ("r-proxy" ,r-proxy)
+ ("r-pscl" ,r-pscl)
+ ("r-purrr" ,r-purrr)
+ ("r-rann" ,r-rann)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppparallel" ,r-rcppparallel)
+ ("r-reshape2" ,r-reshape2)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rhpcblasctl" ,r-rhpcblasctl)
+ ("r-rtsne" ,r-rtsne)
+ ("r-shiny" ,r-shiny)
+ ("r-slam" ,r-slam)
+ ("r-spdep" ,r-spdep)
+ ("r-speedglm" ,r-speedglm)
+ ("r-stringr" ,r-stringr)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-uwot" ,r-uwot)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/cole-trapnell-lab/monocle3")
+ (synopsis "Analysis toolkit for single-cell RNA-Seq data")
+ (description
+ "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
+ (license license:expat)))
+
(define-public r-noiseq
(package
(name "r-noiseq")