GNU bug report logs - #56268
[PATCH] gnu: Add r-bambu.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-bambu.
Date: Tue, 28 Jun 2022 00:17:52 +0200

* 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

Message #10 received at 56268-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 56268-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-bambu.
Date: Thu, 27 Oct 2022 16:01:42 +0200

Applied with minor changes.  Thanks!

-- 
Ricardo

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