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spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.65 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=YvJkqUvu; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 81D76E0F5 X-Spam-Score: 7.65 X-Migadu-Scanner: scn0.migadu.com X-TUID: njnKGdWC/mfA * 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