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-rw-r--r--gnu/packages/bioconductor.scm55
1 files changed, 55 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 782b769225..af7259330c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1965,3 +1965,58 @@ interactive exploration of results.")
"This package provides methods and models for handling zero-inflated
single cell assay data.")
(license license:gpl2+)))
+
+(define-public r-monocle
+ (package
+ (name "r-monocle")
+ (version "2.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "monocle" version))
+ (sha256
+ (base32
+ "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocviews" ,r-biocviews)
+ ("r-cluster" ,r-cluster)
+ ("r-combinat" ,r-combinat)
+ ("r-ddrtree" ,r-ddrtree)
+ ("r-densityclust" ,r-densityclust)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fastica" ,r-fastica)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hsmmsinglecell" ,r-hsmmsinglecell)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-limma" ,r-limma)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plyr" ,r-plyr)
+ ("r-proxy" ,r-proxy)
+ ("r-qlcmatrix" ,r-qlcmatrix)
+ ("r-rann" ,r-rann)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rtsne" ,r-rtsne)
+ ("r-slam" ,r-slam)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-vgam" ,r-vgam)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://bioconductor.org/packages/monocle")
+ (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
+ (description
+ "Monocle performs differential expression and time-series analysis for
+single-cell expression experiments. It orders individual cells according to
+progress through a biological process, without knowing ahead of time which
+genes define progress through that process. Monocle also performs
+differential expression analysis, clustering, visualization, and other useful
+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)))