From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: 58806@debbugs.gnu.org
Subject: [bug#58806] [PATCH] gnu: Add r-baalchip.
Date: Thu, 27 Oct 2022 00:38:09 +0200 [thread overview]
Message-ID: <20221026223809.29865-1-madalinionel.patrascu@mdc-berlin.de> (raw)
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioconductor.scm (r-baalchip): New variable.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3692bb94af..23991983da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2293,6 +2293,51 @@ (define-public r-antiprofiles
tumor samples from healthy controls.")
(license license:artistic2.0)))
+(define-public r-baalchip
+ (package
+ (name "r-baalchip")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BaalChIP" version))
+ (sha256
+ (base32
+ "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
+ (properties `((upstream-name . "BaalChIP")))
+ (build-system r-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (inputs (list perl)) ;; extra/get.overlaps.v2_chrXY.perl
+ (propagated-inputs
+ (list r-coda
+ r-doby
+ r-doparallel
+ r-foreach
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-reshape2
+ r-rsamtools
+ r-scales))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/BaalChIP")
+ (synopsis
+ "Analysis of allele-specific transcription factor binding in cancer genomes")
+ (description
+ "The package offers functions to process multiple @code{ChIP-seq BAM} files
+and detect allele-specific events. Computes allele counts at individual variants
+(SNPs/SNVs), implements extensive @dfn{QC} (quality control) steps to remove
+problematic variants, and utilizes a Bayesian framework to identify statistically
+significant allele-specific events. @code{BaalChIP} is able to account for copy
+number differences between the two alleles, a known phenotypical feature of cancer
+samples.")
+ (license license:artistic2.0)))
+
(define-public r-biocversion
(package
(name "r-biocversion")
base-commit: a2e4e3489b4fdec6e270c93fcd9724abe983217e
--
2.37.3
next reply other threads:[~2022-10-26 22:40 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-10-26 22:38 Mădălin Ionel Patrașcu [this message]
2022-10-27 11:55 ` bug#58806: [PATCH] gnu: Add r-baalchip Ricardo Wurmus
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