From 2ab5d08fbe084f6dc9543545fb13f0791a7be74a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 3 Aug 2021 10:40:47 +0200
Subject: gnu: Add r-spectre.

* gnu/packages/bioinformatics.scm (r-spectre): New variable.
---
 gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 742b02cb5b..910a79c3e3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14806,3 +14806,75 @@ ploidy and allele-specific copy number profiles.")
 copy number estimation, as described by
 @url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
    (license license:gpl3)))
+
+(define-public r-spectre
+  (let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a")
+        (revision "1"))
+    (package
+      (name "r-spectre")
+      (version (git-version "0.5.5" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ImmuneDynamics/Spectre")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0g38grrhbqqa4bmcilvdyawbkcnax6k4vffx2giywp18mbirmj0x"))))
+      (properties `((upstream-name . "Spectre")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-biobase" ,r-biobase)
+         ("r-biocmanager" ,r-biocmanager)
+         ("r-caret" ,r-caret)
+         ("r-class" ,r-class)
+         ("r-colorramps" ,r-colorramps)
+         ("r-data-table" ,r-data-table)
+         ("r-devtools" ,r-devtools)
+         ("r-dplyr" ,r-dplyr)
+         ("r-exactextractr" ,r-exactextractr)
+         ("r-factoextra" ,r-factoextra)
+         ("r-flowcore" ,r-flowcore)
+         ("r-flowsom" ,r-flowsom)
+         ("r-flowviz" ,r-flowviz)
+         ("r-fnn" ,r-fnn)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-ggpointdensity" ,r-ggpointdensity)
+         ("r-ggpubr" ,r-ggpubr)
+         ("r-ggraph" ,r-ggraph)
+         ("r-ggthemes" ,r-ggthemes)
+         ("r-gridextra" ,r-gridextra)
+         ("r-gridextra" ,r-gridextra)
+         ("r-gtools" ,r-gtools)
+         ("r-hdf5array" ,r-hdf5array)
+         ("r-irlba" ,r-irlba)
+         ("r-pheatmap" ,r-pheatmap)
+         ("r-plyr" ,r-plyr)
+         ("r-qs" ,r-qs)
+         ("r-raster" ,r-raster)
+         ("r-rcolorbrewer" ,r-rcolorbrewer)
+         ("r-rgeos" ,r-rgeos)
+         ("r-rhdf5" ,r-rhdf5)
+         ("r-rstudioapi" ,r-rstudioapi)
+         ("r-rsvd" ,r-rsvd)
+         ("r-rtsne" ,r-rtsne)
+         ("r-s2" ,r-s2)
+         ("r-scales" ,r-scales)
+         ("r-sf" ,r-sf)
+         ("r-sp" ,r-sp)
+         ("r-stars" ,r-stars)
+         ("r-stringr" ,r-stringr)
+         ("r-tidygraph" ,r-tidygraph)
+         ("r-tidyr" ,r-tidyr)
+         ("r-tidyr" ,r-tidyr)
+         ("r-tiff" ,r-tiff)
+         ("r-umap" ,r-umap)))
+      (home-page "https://github.com/ImmuneDynamics/Spectre")
+      (synopsis "High-dimensional cytometry and imaging analysis")
+      (description
+       "This package provides a computational toolkit in R for the
+integration, exploration, and analysis of high-dimensional single-cell
+cytometry and imaging data.")
+      (license license:expat))))
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