From 2794caed7c813f2ec4249236de36eaccafee8361 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 12 Jul 2023 21:34:07 +0200
Subject: gnu: Add r-numbat.

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

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9342c44474..341731d066 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -875,6 +875,78 @@ attributes of microbiome data - zero-inflation and over-dispersion, are
 simultaneously considered.")
       (license license:gpl3))))
 
+(define-public r-numbat
+  (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295")
+        (revision "1"))
+    (package
+      (name "r-numbat")
+      (version (git-version "1.3.2-1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/kharchenkolab/numbat")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0wa2cz5iy570r2a57bd74jramxayvfhmxznb0vq4vyk1ia8l5jd1"))))
+      (properties `((upstream-name . "numbat")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-ape
+             r-catools
+             r-data-table
+             r-dendextend
+             r-dplyr
+             r-genomicranges
+             r-ggplot2
+             r-ggraph
+             r-ggtree
+             r-glue
+             r-igraph
+             r-iranges
+             r-logger
+             r-magrittr
+             r-matrix
+             r-optparse
+             r-paralleldist
+             r-patchwork
+             r-pryr
+             r-purrr
+             r-r-utils
+             r-rcpp
+             r-rcpparmadillo
+             r-rhpcblasctl
+             r-roptim
+             r-scales
+             r-scistreer
+             r-stringr
+             r-tibble
+             r-tidygraph
+             r-tidyr
+             r-vcfr
+             r-zoo))
+      (home-page "https://github.com/kharchenkolab/numbat")
+      (synopsis "Haplotype-Aware CNV Analysis from scRNA-Seq")
+      (description
+       "This package provides a computational method that infers copy number
+variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor
+phylogeny.  numbat integrates signals from gene expression, allelic ratio, and
+population haplotype structures to accurately infer allele-specific CNVs in
+single cells and reconstruct their lineage relationship.  numbat can be used
+to:
+
+@enumerate
+@item detect allele-specific copy number variations from single-cells;
+@item differentiate tumor versus normal cells in the tumor microenvironment;
+@item infer the clonal architecture and evolutionary history of profiled
+tumors.
+@end enumerate
+
+numbat does not require tumor/normal-paired DNA or genotype data, but operates
+solely on the donor scRNA-data data (for example, 10x Cell Ranger output).")
+      (license license:expat))))
+
 (define-public r-p2data
   (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c")
         (revision "1"))
-- 
cgit 1.4.1