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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