Subject: [PATCH] gnu: Add r-psupertime.
From: Navid Afkhami <[email-masked]>
To: <[email-masked]>
Date: Fri, 3 Feb 2023 14:44:02 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/bioinformatics.scm (r-psupertime): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b8676b0ece..703d71fb68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8229,6 +8229,50 @@ (define-public r-doubletcollection
 benchmark of those eight mentioned methods.")
       (license license:gpl3+))))
 
+(define-public r-psupertime
+  (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207")
+        (revision "1"))
+    (package
+      (name "r-psupertime")
+      (version (git-version "0.2.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wmacnair/psupertime")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh"))))
+      (properties `((upstream-name . "psupertime")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-cowplot
+                               r-data-table
+                               r-fastcluster
+                               r-forcats
+                               r-ggplot2
+                               r-glmnet
+                               r-knitr
+                               r-matrix
+                               r-rcolorbrewer
+                               r-scales
+                               r-scran
+                               r-singlecellexperiment
+                               r-stringr
+                               r-summarizedexperiment
+                               r-topgo))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/wmacnair/psupertime")
+      (synopsis
+       "Psupertime is supervised pseudotime for single cell RNAseq data")
+      (description
+       "Psupertime uses single cell RNAseq data, where the cells have a known ordering.
+This ordering helps to identify a small number of genes which place
+cells in that known order.  It can be used for discovery of relevant
+genes, for identification of subpopulations, and characterization of
+further unknown or differently labelled data.")
+      (license license:gpl3))))
+
 (define-public r-pando
   (package
     (name "r-pando")
-- 
2.34.1