bug#55148: closed ([PATCH] gnu: Add r-agilp.)

[GNU bug Tracking System]

Your message dated Wed, 27 Apr 2022 16:36:42 +0200
with message-id <8735hy4mn8.fsf@elephly.net>
and subject line Re: [bug#55148] [PATCH] gnu: Add r-agilp.
has caused the debbugs.gnu.org bug report #55148,
regarding [PATCH] gnu: Add r-agilp.
to be marked as done.

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-- 
55148: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=55148
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-agilp.
>
>
>
>
> Date: 
>
> Wed, 27 Apr 2022 14:50:15 +0200
>
>
>
>
> * gnu/packages/bioconductor.scm (r-agilp): New variable.
> ---
>  gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
>  1 file changed, 44 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index 67ee6079c6..c0d874b423 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -1664,6 +1664,50 @@ (define-public r-adamgui
>  the @code{GFAGpathUi} function.")
>      (license license:gpl2+)))
>  
> +(define-public r-agilp
> +  (package
> +    (name "r-agilp")
> +    (version "3.26.0")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (bioconductor-uri "agilp" version))
> +              (sha256
> +               (base32
> +                "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp"))))
> +    (properties `((upstream-name . "agilp")))
> +    (build-system r-build-system)
> +    (home-page "https://bioconductor.org/packages/agilp";)
> +    (synopsis "Processing of Agilent expression array")
> +    (description
> +      "This package @code{agilp} was developed to provide a pipeline for the
> +low-level analysis of gene expression microarray data, primarily focused on the
> +Agilent platform, but which also provides utilities which may be useful for
> +other platforms.  @code{Agilp} implements functions like:
> +@itemize
> +@item
> +@code{AAProcess}: extracts raw expression data from Agilent expression array
> +scanner files;
> +@item
> +@code{filenamex}: a file name listing utility;
> +@item
> +@code{Baseline}: constructs a file with the mean of each probe from a set of 
> raw
> +expression array data files
> +@item
> +@code{Loader}: selects a set of processed array files from directory according
> +to criteria from a template file;
> +@item
> +@code{AALoess}: normalises a set of gene expression data files using 
> @code{LOESS}
> +against a reference data set;
> +@item
> +@code{IDswop}: maps expression data across different bioinformatic identifiers;
> +@item
> +@code{Equaliser}: trims a set of gene expression data files to include only the
> +set of identifiers common to all files.
> +@end itemize")
> +    ;; Some files are under GPLv2+ but the combined work is released under the
> +    ;; GPLv3.
> +    (license license:gpl3)))
> +
>  (define-public r-aneufinder
>    (package
>      (name "r-aneufinder")
>
> base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76
> -- 
> 2.34.0
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#55148] [PATCH] gnu: Add r-agilp.
>
>
>
>
> Date: 
>
> Wed, 27 Apr 2022 16:36:42 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.6.10; emacs 28.0.50
>
>
>
>
> Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
>
> > * gnu/packages/bioconductor.scm (r-agilp): New variable.
>
> Thank you.  I applied it after trimming the description, because all
> that detail was probably a little much.
>
> -- 
> Ricardo
>
>
> --- End Message ---