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[bug#56819] [PATCH 2/2] gnu: Add r-infercnv.
From: |
Mădălin Ionel Patrașcu |
Subject: |
[bug#56819] [PATCH 2/2] gnu: Add r-infercnv. |
Date: |
Thu, 28 Jul 2022 23:38:59 +0200 |
* gnu/packages/bioconductor.scm (r-infercnv): New variable.
---
gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 31484799b2..e9bfbed9b5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages python)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
@@ -2647,6 +2648,65 @@ (define-public r-ideoviz
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
+(define-public r-infercnv
+ (package
+ (name "r-infercnv")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "infercnv" version))
+ (sha256
+ (base32
+ "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
+ (properties `((upstream-name . "infercnv")))
+ (build-system r-build-system)
+ (inputs (list python))
+ (propagated-inputs
+ (list r-ape
+ r-argparse
+ r-biocgenerics
+ r-catools
+ r-coda
+ r-coin
+ r-digest
+ r-doparallel
+ r-dplyr
+ r-edger
+ r-fastcluster
+ r-fitdistrplus
+ r-foreach
+ r-futile-logger
+ r-future
+ r-ggplot2
+ r-gplots
+ r-gridextra
+ r-hiddenmarkov
+ r-leiden
+ r-matrix
+ r-paralleldist
+ r-phyclust
+ r-rann
+ r-rcolorbrewer
+ r-reshape
+ r-rjags
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/broadinstitute/inferCNV/wiki")
+ (synopsis "Infer copy number variation from single-cell RNA-Seq data")
+ (description
+ "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to
identify
+evidence for somatic large-scale chromosomal copy number alterations, such as
gains
+or deletions of entire chromosomes or large segments of chromosomes. This is
done
+by exploring expression intensity of genes across positions of a tumor genome
in
+comparison to a set of reference \"normal\" cells. A heatmap is generated
+illustrating the relative expression intensities across each chromosome, and it
+often becomes readily apparent as to which regions of the tumor genome are
+over-abundant or less-abundant as compared to that of normal cells.")
+ (license license:bsd-3)))
+
(define-public r-iranges
(package
(name "r-iranges")
--
2.37.1