Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity and 'WeightedCluster' <doi:10.12682/lives.2296-1658.2013.24> <https://mephisto.unige.ch/weightedcluster/> for weighted clustering on metacells. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.
| Version: | 1.1 |
| Depends: | R (≥ 4.0.0) |
| Imports: | igraph,RANN,corpcor,weights,Hmisc,Matrix,matrixStats,plyr,irlba, grDevices,patchwork,ggplot2,umap,entropy,Rtsne,dbscan,scales,plotfunctions,proxy, methods,rlang |
| Suggests: | SingleCellExperiment,SummarizedExperiment,cowplot,scater,Seurat,knitr,rmarkdown,remotes,bluster, velocyto.R,WeightedCluster,testthat (≥ 3.0.0) |
| Published: | 2025-12-16 |
| DOI: | 10.32614/CRAN.package.SuperCell |
| Author: | Mariia Bilous [aut], Matei Teleman [cre] |
| Maintainer: | Matei Teleman <matei.teleman at unil.ch> |
| BugReports: | https://github.com/GfellerLab/SuperCell/issues |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Additional_repositories: | https://mteleman.github.io/drat2 |
| Materials: | README |
| CRAN checks: | SuperCell results |
| Reference manual: | SuperCell.html ,SuperCell.pdf |
| Vignettes: | Example of the SuperCell pipeline (source,R code) Combined or independent SuperCell runs for different samples (source,R code) |
| Package source: | SuperCell_1.1.tar.gz |
| Windows binaries: | r-devel:SuperCell_1.0.1.zip, r-release:SuperCell_1.0.1.zip, r-oldrel:SuperCell_1.0.1.zip |
| macOS binaries: | r-release (arm64):SuperCell_1.1.tgz, r-oldrel (arm64):SuperCell_1.1.tgz, r-release (x86_64):SuperCell_1.1.tgz, r-oldrel (x86_64):SuperCell_1.1.tgz |
| Old sources: | SuperCell archive |
| Reverse imports: | SuperCellCyto |
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