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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 |
Please use the canonical form https://CRAN.R-project.org/package=SoupX to link to this page.
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.