bug#56161: closed ([PATCH] gnu: Add r-atena.)

[GNU bug Tracking System]

Your message dated Mon, 31 Oct 2022 21:40:53 +0100
with message-id <87edund8v1.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-atena.
has caused the debbugs.gnu.org bug report #56161,
regarding [PATCH] gnu: Add r-atena.
to be marked as done.

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-- 
56161: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56161
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-atena.
>
>
>
>
> Date: 
>
> Thu, 23 Jun 2022 12:25:20 +0200
>
>
>
>
> * 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
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-atena.
>
>
>
>
> Date: 
>
> Mon, 31 Oct 2022 21:40:53 +0100
>
>
>
>
> User-agent: 
>
> mu4e 1.8.9; emacs 28.1
>
>
>
>
> Applied, thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---