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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. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.
| Version: | 1.0 |
| Depends: | R (≥ 4.0.0) |
| Imports: | igraph, RANN, WeightedCluster, 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, testthat (≥ 3.0.0) |
| Published: | 2024-09-05 |
| DOI: | 10.32614/CRAN.package.SuperCell |
| Author: | Mariia Bilous [aut], Leonard Herault [cre] |
| Maintainer: | Leonard Herault <leonard.herault at unil.ch> |
| BugReports: | https://github.com/GfellerLab/SuperCell/issues |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Additional_repositories: | https://mteleman.github.io/drat |
| Materials: | README |
| CRAN checks: | SuperCell results |
| Reference manual: | 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_1.0.tar.gz |
| Windows binaries: | r-devel: SuperCell_1.0.zip, r-release: SuperCell_1.0.zip, r-oldrel: SuperCell_1.0.zip |
| macOS binaries: | r-release (arm64): SuperCell_1.0.tgz, r-oldrel (arm64): SuperCell_1.0.tgz, r-release (x86_64): SuperCell_1.0.tgz, r-oldrel (x86_64): SuperCell_1.0.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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