Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
| Version: | 1.6.2 |
| Depends: | R (≥ 3.5.0) |
| Imports: | ggplot2, Matrix, methods, Seurat (≥ 3.2.2) |
| Suggests: | knitr, rstan, DropletUtils, rmarkdown, formatR |
| Published: | 2022-11-01 |
| DOI: | 10.32614/CRAN.package.SoupX |
| Author: | Matthew Daniel Young |
| Maintainer: | Matthew Daniel Young <my4 at sanger.ac.uk> |
| License: | GPL-2 |
| URL: | https://github.com/constantAmateur/SoupX |
| NeedsCompilation: | no |
| Citation: | SoupX citation info |
| Materials: | README |
| In views: | Omics |
| CRAN checks: | SoupX results |
| Reference manual: | SoupX.pdf |
| Vignettes: |
PBMC Demonstration |
| Package source: | SoupX_1.6.2.tar.gz |
| Windows binaries: | r-devel: SoupX_1.6.2.zip, r-release: SoupX_1.6.2.zip, r-oldrel: SoupX_1.6.2.zip |
| macOS binaries: | r-release (arm64): SoupX_1.6.2.tgz, r-oldrel (arm64): SoupX_1.6.2.tgz, r-release (x86_64): SoupX_1.6.2.tgz, r-oldrel (x86_64): SoupX_1.6.2.tgz |
| Old sources: | SoupX archive |
| Reverse imports: | singleCellTK |
| Reverse suggests: | CRMetrics |
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