[bug#28029] [PATCH 1/2] gnu: Add r-dexseq.

[Roel Janssen <roel@gnu.org>]

Ricardo Wurmus writes:

> * gnu/packages/bioinformatics.scm (r-dexseq): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 02b338be6..478a756fb 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5791,6 +5791,49 @@ differential expression based on a model using the negative binomial
>  distribution.")
>      (license license:lgpl3+)))
>  
> +(define-public r-dexseq
> +  (package
> +    (name "r-dexseq")
> +    (version "1.22.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (bioconductor-uri "DEXSeq" version))
> +       (sha256
> +        (base32
> +         "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
> +    (properties `((upstream-name . "DEXSeq")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +     `(("r-annotationdbi" ,r-annotationdbi)
> +       ("r-biobase" ,r-biobase)
> +       ("r-biocgenerics" ,r-biocgenerics)
> +       ("r-biocparallel" ,r-biocparallel)
> +       ("r-biomart" ,r-biomart)
> +       ("r-deseq2" ,r-deseq2)
> +       ("r-genefilter" ,r-genefilter)
> +       ("r-geneplotter" ,r-geneplotter)
> +       ("r-genomicranges" ,r-genomicranges)
> +       ("r-hwriter" ,r-hwriter)
> +       ("r-iranges" ,r-iranges)
> +       ("r-rcolorbrewer" ,r-rcolorbrewer)
> +       ("r-rsamtools" ,r-rsamtools)
> +       ("r-s4vectors" ,r-s4vectors)
> +       ("r-statmod" ,r-statmod)
> +       ("r-stringr" ,r-stringr)
> +       ("r-summarizedexperiment" ,r-summarizedexperiment)))
> +    (home-page "http://bioconductor.org/packages/DEXSeq")
> +    (synopsis "Inference of differential exon usage in RNA-Seq")
> +    (description
> +     "This package is focused on finding differential exon usage using RNA-seq
> +exon counts between samples with different experimental designs.  It provides
> +functions that allows the user to make the necessary statistical tests based
> +on a model that uses the negative binomial distribution to estimate the
> +variance between biological replicates and generalized linear models for
> +testing.  The package also provides functions for the visualization and
> +exploration of the results.")
> +    (license license:gpl3+)))
> +
>  (define-public r-annotationforge
>    (package
>      (name "r-annotationforge")

I have an almost identical package, so LGTM!

Kind regards,
Roel Janssen