* [bug#66530] [PATCH] gnu: Add r-metacell.
@ 2023-10-13 16:14 Afkhami, Navid
2023-10-17 12:33 ` bug#66530: " Ricardo Wurmus
0 siblings, 1 reply; 2+ messages in thread
From: Afkhami, Navid @ 2023-10-13 16:14 UTC (permalink / raw)
To: 66530; +Cc: Afkhami, Navid
* 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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* bug#66530: [PATCH] gnu: Add r-metacell.
2023-10-13 16:14 [bug#66530] [PATCH] gnu: Add r-metacell Afkhami, Navid
@ 2023-10-17 12:33 ` Ricardo Wurmus
0 siblings, 0 replies; 2+ messages in thread
From: Ricardo Wurmus @ 2023-10-17 12:33 UTC (permalink / raw)
To: 66530-done
Thanks for the patches. I applied them after some massaging.
--
Ricardo
^ permalink raw reply [flat|nested] 2+ messages in thread
end of thread, other threads:[~2023-10-17 12:35 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2023-10-13 16:14 [bug#66530] [PATCH] gnu: Add r-metacell Afkhami, Navid
2023-10-17 12:33 ` bug#66530: " Ricardo Wurmus
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).