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02/05: gnu: Add r-bambu.
From: |
guix-commits |
Subject: |
02/05: gnu: Add r-bambu. |
Date: |
Thu, 27 Oct 2022 10:00:31 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 9b337c2735f522a8fcaa1e7972df4a76f97d29b8
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Tue Jun 28 00:17:52 2022 +0200
gnu: Add r-bambu.
* 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 7aef32286a..3a53ebdf95 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2455,6 +2455,49 @@ files. The whole genome may be considered as well as a
set of target regions.
Various visual and textual types of output are available.")
(license license:lgpl3)))
+(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 R package is for multi-sample transcript discovery and
+quantification using long read RNA-Seq data. You can use bambu after read
+alignment to obtain expression estimates for known and novel transcripts and
+genes. The output from 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")