bug#66530: closed ([PATCH] gnu: Add r-metacell.)

[GNU bug Tracking System]

Your message dated Tue, 17 Oct 2023 14:33:33 +0200
with message-id <87mswhjumh.fsf@elephly.net>
and subject line [PATCH] gnu: Add r-metacell.
has caused the debbugs.gnu.org bug report #66530,
regarding [PATCH] gnu: Add r-metacell.
to be marked as done.

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-- 
66530: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=66530
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-metacell.
>
>
>
>
> Date: 
>
> Fri, 13 Oct 2023 16:14:43 +0000
>
>
>
>
> * gnu/packages/bioinformatics.scm (r-metacell): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++
>  1 file changed, 60 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index cb0bdf766e..45afde699d 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -10285,6 +10285,66 @@ (define-public r-markdownreports
>  discovered.")
>        (license license:gpl3))))
>  
> +(define-public r-metacell
> +  (let ((commit "d6a6926d103ee0cb34a611c753572429c94a53d9")
> +        (revision "1"))
> +    (package
> +      (name "r-metacell")
> +      (version (git-version "0.3.41" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/tanaylab/metacell/";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "0zrsckr3y35x37mj3ibm6scyqx925s84wzrz1i42fnm9n3msc265"))))
> +      (properties `((upstream-name . "metacell")))
> +      (build-system r-build-system)
> +      (propagated-inputs (list r-cluster
> +                               r-cowplot
> +                               r-data-table
> +                               r-dbscan
> +                               r-domc
> +                               r-dplyr
> +                               r-entropy
> +                               r-ggplot2
> +                               r-graph
> +                               r-igraph
> +                               r-kernsmooth
> +                               r-magrittr
> +                               r-matrix
> +                               r-matrixstats
> +                               r-pdist
> +                               r-pheatmap
> +                               r-plyr
> +                               r-rcolorbrewer
> +                               r-rcurl
> +                               r-rgraphviz
> +                               r-slam
> +                               r-singlecellexperiment
> +                               r-svglite
> +                               r-tgconfig
> +                               r-tgstat
> +                               r-tgutil
> +                               r-tidyr
> +                               r-umap
> +                               r-umap
> +                               r-zoo))
> +      (native-inputs (list r-knitr))
> +      (home-page "https://github.com/tanaylab/metacell/";)
> +      (synopsis "Meta cell analysis for single cell RNA-seq data")
> +      (description
> +       "This package facilitates the analysis of single-cell RNA-seq UMI 
> matrices.
> +It does this by computing partitions of a cell similarity graph into
> +small homogeneous groups of cells, which are defined as metacells (MCs).
> +The derived MCs are then used for building different representations of
> +the data, allowing matrix or 2D graph visualization forming a basis for
> +analysis of cell types, subtypes, transcriptional gradients,cell-cycle
> +variation, gene modules and their regulatory models and more.")
> +      (license license:expat))))
> +
>  (define-public r-snapatac
>    (package
>      (name "r-snapatac")
>
> base-commit: dcfd4d9c4827ca6bfebeec46fe6bb8373c425a1c
> prerequisite-patch-id: 8b3f1b30e7ca1f6ddb21bf801faad91cce276dfd
> prerequisite-patch-id: 86f04eb38885c80e1fa302cec734581778e62c26
> prerequisite-patch-id: d5cebe9646097c611915c8b796a94ff0d1831343
> prerequisite-patch-id: 675ed63512dcf5b145a929d0097b1bb7e7f1c389
> prerequisite-patch-id: 8a7046dfe2c6c18892fed37a877f66be5be7f96e
> -- 
> 2.34.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add r-metacell.
>
>
>
>
> Date: 
>
> Tue, 17 Oct 2023 14:33:33 +0200
>
>
>
>
> User-agent: 
>
> mu4e 1.10.7; emacs 29.1
>
>
>
>
> Thanks for the patches.  I applied them after some massaging.
>
> -- 
> Ricardo
>
>
> --- End Message ---