From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: 56268@debbugs.gnu.org
Subject: [bug#56268] [PATCH] gnu: Add r-bambu.
Date: Tue, 28 Jun 2022 00:17:52 +0200 [thread overview]
Message-ID: <20220627221752.20017-1-madalinionel.patrascu@mdc-berlin.de> (raw)
* gnu/packages/bioconductor.scm (r-bambu): New variable.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..7d8df496eb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2029,6 +2029,49 @@ (define-public r-aneufinder
sequencing data.")
(license license:artistic2.0)))
+(define-public r-bambu
+ (package
+ (name "r-bambu")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bambu" version))
+ (sha256
+ (base32
+ "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w"))))
+ (properties `((upstream-name . "bambu")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biocparallel
+ r-bsgenome
+ r-data-table
+ r-dplyr
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rcpp
+ r-rcpparmadillo
+ r-rsamtools
+ r-s4vectors
+ r-summarizedexperiment
+ r-tidyr
+ r-xgboost))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/GoekeLab/bambu")
+ (synopsis
+ "Isoform reconstruction and quantification for long read RNA-Seq data")
+ (description
+ "This @code{R} package is for multi-sample transcript discovery and
+quantification using long read RNA-Seq data. You can use @code{bambu} after
+read alignment to obtain expression estimates for known and novel transcripts
+and genes. The output from @code{bambu} can directly be used for visualisation
+and downstream analysis, such as differential gene expression or transcript
+usage.")
+ (license license:gpl3)))
+
(define-public r-biocversion
(package
(name "r-biocversion")
base-commit: 144a750f8b10e606751bc887bcb09e7fb7ae09ff
--
2.36.1
next reply other threads:[~2022-06-27 22:19 UTC|newest]
Thread overview: 2+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-06-27 22:17 Mădălin Ionel Patrașcu [this message]
2022-10-27 14:01 ` bug#56268: [PATCH] gnu: Add r-bambu Ricardo Wurmus
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