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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 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

Documentation:

Reference manual: SoupX.pdf
Vignettes: PBMC Demonstration

Downloads:

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 dependencies:

Reverse imports: singleCellTK
Reverse suggests: CRMetrics

Linking:

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.