[PATCH 35/35] gnu: Add r-seurat.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <address@hidden>

* 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