GNU bug report logs - #59142
[PATCH] gnu: Add r-pals, r-glmnetutils and r-pando.

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Message #11 received at 59142 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <59142 <at> debbugs.gnu.org>
Subject: [PATCH 3/3] gnu: Add r-pando.
Date: Wed, 9 Nov 2022 04:13:31 +0100

* gnu/packages/bioinformatics.scm (r-pando): New variable.
---
 gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 47f5574eeb..87c93bab4d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7600,6 +7600,56 @@ (define-public r-chromunity
 Pore-C concatemers.")
       (license license:gpl3))))
 
+(define-public r-pando
+  (package
+    (name "r-pando")
+    (version "1.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+            (url "https://github.com/quadbiolab/Pando")
+            (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0c83anzdrbvg47p9xns2bxpjlx5z328can3jmzilw6rygwp7hyii"))))
+    (properties `((upstream-name . "Pando")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bayestestr
+           r-brms
+           r-foreach
+           r-genomicranges
+           r-ggplot2
+           r-ggpointdensity
+           r-ggraph
+           r-glmnetutils
+           r-iranges
+           r-irlba
+           r-matrix
+           r-motifmatchr
+           r-pals
+           r-patchwork
+           r-seurat
+           r-signac
+           r-sparsematrixstats
+           r-tfbstools
+           r-tidygraph
+           r-tidyverse
+           r-uwot
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/quadbiolab/Pando")
+    (synopsis
+     "Inferring regulomes from multi-modal single-cell genomics data")
+    (description
+     "@code{Pando} leverages multi-modal single-cell measurements to infer gene
+regulatory networks using a flexible linear model-based framework.  By modeling
+the relationship between TF-binding site pairs with the expression of target
+genes, @code{Pando} simultaneously infers gene modules and sets of regulatory
+regions for each transcription factor.")
+    (license license:expat)))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
-- 
2.38.1

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