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authorMădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>2022-06-28 00:17:52 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-10-27 15:51:55 +0200
commit9b337c2735f522a8fcaa1e7972df4a76f97d29b8 (patch)
tree1eec20fa121dd41e71e888bb856d1e70000198a4
parentf0d0b6a0c5e3cc5d7232ef16c5ded3dfc458bf01 (diff)
gnu: Add r-bambu.
* gnu/packages/bioconductor.scm (r-bambu): New variable.
-rw-r--r--gnu/packages/bioconductor.scm43
1 files changed, 43 insertions, 0 deletions
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")