(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20221219150341.2823150-1-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-cardelino): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
Toggle diff (53 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ec1bbb99d1..2d8b475b2a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3480,6 +3480,44 @@ (define-public r-biocgenerics
packages.")
(license license:artistic2.0)))
+(define-public r-cardelino
+ (package
+ (name "r-cardelino")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "cardelino" version))
+ (sha256
+ (base32
+ "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs"))))
+ (properties `((upstream-name . "cardelino")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-combinat
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-ggtree
+ r-matrix
+ r-matrixstats
+ r-pheatmap
+ r-s4vectors
+ r-snpstats
+ r-variantannotation
+ r-vcfr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/single-cell-genetics/cardelino")
+ (synopsis "Clone Identification from Single Cell Data")
+ (description
+ "This package provides methods to infer clonal tree configuration for a
+population of cells using single-cell RNA-seq data (scRNA-seq), and possibly
+other data modalities. Methods are also provided to assign cells to inferred
+clones and explore differences in gene expression between clones. These
+methods can flexibly integrate information from imperfect clonal trees
+inferred based on bulk exome-seq data, and sparse variant alleles expressed in
+scRNA-seq data. A flexible beta-binomial error model that accounts for
+stochastic dropout events as well as systematic allelic imbalance is used.")
+ (license license:gpl3)))
+
(define-public r-coverageview
(package
(name "r-coverageview")
base-commit: 513ab9956ddfd54cfb411c73cfd0838b78b47fc4
--
2.38.1