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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: 6.14 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=Eun51gk2; 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: 5A93E3812E X-Spam-Score: 6.14 X-Migadu-Scanner: scn0.migadu.com X-TUID: FZr7bL11pdQp * gnu/packages/bioconductor.scm (r-atena): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..5ec69365d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,47 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-atena + (package + (name "r-atena") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atena" version)) + (sha256 + (base32 + "1jbnlxrk8npflym008cgrazamlsh6y624g1d6x648kcjd8zwvj6n")))) + (properties `((upstream-name . "atena"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-s4vectors + r-scales + r-sparsematrixstats + r-squarem + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/functionalgenomics/atena") + (synopsis "Analysis of transposable elements") + (description + "The @code{atena} package quantifies expression of @dfn{TEs} (transposable +elements) from RNA-seq data through different methods, including @code{ERVmap}, +@code{TEtranscripts} and @code{Telescope}. A common interface is provided to +use each of these methods, which consists of building a parameter object, calling +the quantification function with this object and getting a +@code{SummarizedExperiment} object as an output container of the quantified +expression profiles. The implementation allows quantifing TEs and gene +transcripts in an integrated manner.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1