diff options
| author | Afkhami, Navid <Navid.Afkhami@mdc-berlin.de> | 2023-10-13 16:14:43 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-10-17 14:25:36 +0200 |
| commit | 48f9484483a6f5c4a12ac3dc8e8cd1e26df58f9b (patch) | |
| tree | 3fef97694ab339e7911c2da48200ef5c52f3bd46 /gnu/packages | |
| parent | 54274a5a3bb5e2f637758d1d8797213d1ebaec20 (diff) | |
gnu: Add r-metacell.
* gnu/packages/bioinformatics.scm (r-metacell): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 60 insertions, 0 deletions
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 @@ figures. This tool will create clean markdown reports about what you just 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") |