From: Simon Tournier <zimon.toutoune@gmail.com>
To: 60885@debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune@gmail.com>
Subject: [bug#60885] [PATCH 4/4] gnu: Add r-numbat.
Date: Tue, 17 Jan 2023 18:30:41 +0100 [thread overview]
Message-ID: <20230117173041.1851206-4-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20230117173041.1851206-1-zimon.toutoune@gmail.com>
* gnu/packages/bioconductor.scm (r-numbat): New variable.
---
gnu/packages/bioconductor.scm | 67 +++++++++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3511bfd81a..2d6093b238 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6696,6 +6696,73 @@ (define-public r-mzr
previously been used in XCMS.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-numbat
+ (package
+ (name "r-numbat")
+ (version "1.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "numbat" version))
+ (sha256
+ (base32
+ "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb"))))
+ (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 (CNV) in cancer scRNA-seq data and reconstructs the tumor
+phylogeny. It 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. It 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). It 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
+
+For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y,
+Gao et al in Nature Biotechnology 2022}.")
+ (license license:expat)))
+
(define-public r-organism-dplyr
(package
(name "r-organism-dplyr")
--
2.38.1
next prev parent reply other threads:[~2023-01-17 17:31 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-01-17 17:26 [bug#60885] [PATCH 0/4] Some bioinfo packages Simon Tournier
2023-01-17 17:30 ` [bug#60885] [PATCH 1/4] gnu: Add python-vireosnp Simon Tournier
2023-01-17 17:30 ` [bug#60885] [PATCH 2/4] gnu: Add r-scistreer Simon Tournier
2023-01-17 17:30 ` [bug#60885] [PATCH 3/4] gnu: Add r-roptim Simon Tournier
2023-01-17 17:30 ` Simon Tournier [this message]
2023-01-20 9:56 ` bug#60885: [PATCH 0/4] Some bioinfo packages Ricardo Wurmus
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