SoupX: Single Cell mRNA Soup eXterminator

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>
License: GPL-2
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:, r-release:, r-oldrel:
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 dependencies:

Reverse imports: singleCellTK
Reverse suggests: CRMetrics


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