From: Raoul Jean Pierre Bonnal <ilpuccio.f...@gmail.com>
* gnu/packages/bioinformatics.scm (r-seurat): New variable.
---
gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 56 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0a77ccf..ea64002 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8504,3 +8504,59 @@ a specified false discovery rate. It also contains a
number of utilities to
explore the MS/MS results and assess missed and irregular enzymatic cleavages,
mass measurement accuracy, etc.")
(license license:artistic2.0)))
+
+(define-public r-seurat
+ (let ((commit "e1eae2da82ada2211e84fbc471615e8d3921b539"))
+ (package
+ (name "r-seurat")
+ (version (string-append "1.4." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/satijalab/seurat";)
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "03g1bhmlyd8ajsp54n2k3ly6hfrz936cy0ql49l7invaqsv8b130"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-rocr" ,r-rocr)
+ ("r-stringr" ,r-stringr)
+ ("r-rtsne" ,r-rtsne)
+ ("r-reshape2" ,r-reshape2)
+ ("r-igraph" ,r-igraph)
+ ("r-plyr" ,r-plyr)
+ ("r-dplyr" ,r-dplyr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-irlba" ,r-irlba)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gplots" ,r-gplots)
+ ("r-gdata" ,r-gdata)
+ ("r-rcpp" ,r-rcpp)
+ ("r-cowplot" ,r-cowplot)
+ ("r-mixtools" ,r-mixtools)
+ ("r-lars" ,r-lars)
+ ("r-fastica" ,r-fastica)
+ ("r-tsne" ,r-tsne)
+ ("r-fpc" ,r-fpc)
+ ("r-ape" ,r-ape)
+ ("r-vgam" ,r-vgam)
+ ("r-pbapply" ,r-pbapply)
+ ("r-fnn" ,r-fnn)
+ ("r-caret" ,r-caret)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-tclust" ,r-tclust)
+ ("r-ranger" ,r-ranger)))
+ (home-page "http://www.satijalab.org/seurat";)
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and exploration
+of single cell RNA-seq data. It easily enables widely-used analytical
techniques,
+including the identification of highly variable genes, dimensionality
reduction;
+PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density
clustering,
+hierarchical clustering, k-means, and the discovery of differentially expressed
+genes and markers.")
+ (license license:gpl3))))
--
1.9.1
