GNU bug report logs - #60203
[PATCH] gnu: Add r-cardelino.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 60203 in the body.
You can then email your comments to 60203 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH] gnu: Add r-cardelino.
Date: Mon, 19 Dec 2022 16:03:41 +0100

* gnu/packages/bioconductor.scm (r-cardelino): New variable.
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

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

Message #10 received at 60203-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 60203-done <at> debbugs.gnu.org
Subject: Re: [bug#60203] [PATCH] gnu: Add r-cardelino.
Date: Mon, 19 Dec 2022 19:24:02 +0100

zimoun <zimon.toutoune <at> gmail.com> writes:

> * gnu/packages/bioconductor.scm (r-cardelino): New variable.

Applied, thanks!

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.