[debbugs-tracker] bug#28029: closed ([PATCH 1/2] gnu: Add r-dexseq.)

[GNU bug Tracking System]

Your message dated Mon, 14 Aug 2017 12:03:25 +0200
with message-id <address@hidden>
and subject line Re: [bug#28029] [PATCH 1/2] gnu: Add r-dexseq.
has caused the debbugs.gnu.org bug report #28029,
regarding [PATCH 1/2] gnu: Add r-dexseq.
to be marked as done.

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-- 
28029: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=28029
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> --- Begin Message ---
>
>
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> Subject: 
>
> [PATCH 1/2] gnu: Add r-dexseq.
>
>
>
>
> Date: 
>
> Wed, 9 Aug 2017 19:40:22 +0200
>
>
>
>
> * 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")
> -- 
> 2.13.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#28029] [PATCH 1/2] gnu: Add r-dexseq.
>
>
>
>
> Date: 
>
> Mon, 14 Aug 2017 12:03:25 +0200
>
>
>
>
> User-agent: 
>
> mu4e 0.9.18; emacs 25.2.1
>
>
>
>
> Roel Janssen <address@hidden> writes:
>
> > Ricardo Wurmus writes:
> >
> >> * gnu/packages/bioinformatics.scm (r-dexseq): New variable.
> […]
> > I have an almost identical package, so LGTM!
>
> Thanks for verifying the package :) I’ve pushed these two patches to
> master.
>
> -- Ricardo
>
>
> --- End Message ---