bug#56034: closed ([PATCH] gnu: Add r-amaretto.)

[GNU bug Tracking System]

Your message dated Thu, 30 Jun 2022 15:50:59 +0200
with message-id <87mtdu8dk1.fsf@elephly.net>
and subject line Re: [bug#56034] [PATCH] gnu: Add r-amaretto.
has caused the debbugs.gnu.org bug report #56034,
regarding [PATCH] gnu: Add r-amaretto.
to be marked as done.

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-- 
56034: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56034
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-amaretto.
>
>
>
>
> Date: 
>
> Fri, 17 Jun 2022 11:29:29 +0200
>
>
>
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 1e87b190c2..a78ceb2de5 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna
>  objects are used so that other packages could be used as well.")
>      (license license:gpl3)))
>  
> +(define-public r-amaretto
> +  (package
> +    (name "r-amaretto")
> +    (version "1.12.0")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "AMARETTO" version))
> +              (sha256
> +               (base32
> +                "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
> +    (properties `((upstream-name . "AMARETTO")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +     (list r-biocfilecache
> +           r-callr
> +           r-circlize
> +           r-complexheatmap
> +           r-curatedtcgadata
> +           r-doparallel
> +           r-dplyr
> +           r-dt
> +           r-foreach
> +           r-ggplot2
> +           r-glmnet
> +           r-gridextra
> +           r-httr
> +           r-impute
> +           r-knitr
> +           r-limma
> +           r-matrix
> +           r-matrixstats
> +           r-multiassayexperiment
> +           r-rcpp
> +           r-readr
> +           r-reshape2
> +           r-rmarkdown
> +           r-tibble))
> +    (native-inputs (list r-knitr))
> +    (home-page "https://bioconductor.org/packages/AMARETTO";)
> +    (synopsis "Regulatory network inference and driver gene evaluation")
> +    (description
> +     "This package @code{AMARETTO} represents an algorithm that integrates copy
> +number, DNA methylation and gene expression data to identify a set of driver
> +genes by analyzing cancer samples and connects them to clusters of co-expressed
> +genes, which we define as modules.  @code{AMARETTO} can be applied in a 
> pancancer
> +setting to identify cancer driver genes and their modules on multiple cancer
> +sites.  @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
> +and EMT, and modules that accurately predict survival and molecular subtypes.
> +This allows @code{AMARETTO} to identify novel cancer driver genes directing
> +canonical cancer pathways.")
> +    (license license:asl2.0)))
> +
>  (define-public r-aneufinder
>    (package
>      (name "r-aneufinder")
>
> base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
> -- 
> 2.36.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#56034] [PATCH] gnu: Add r-amaretto.
>
>
>
>
> Date: 
>
> Thu, 30 Jun 2022 15:50:59 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.6.11; emacs 28.1
>
>
>
>
> Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
>
> > diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> > index 1e87b190c2..a78ceb2de5 100644
> > --- a/gnu/packages/bioconductor.scm
> > +++ b/gnu/packages/bioconductor.scm
> > @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna
> >  objects are used so that other packages could be used as well.")
> >      (license license:gpl3)))
> >  
> > +(define-public r-amaretto
>
> Applied (with a new commit message).
>
> Thanks!
>
> -- 
> Ricardo
>
>
> --- End Message ---