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A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija (2019) <doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9> for more details.
Version: | 0.4.1 |
Depends: | R (≥ 3.6.0) |
Imports: | dplyr, magrittr, MASS, Matrix (≥ 1.5-0), methods, future.apply, future, ggplot2, reshape2, rlang, gridExtra, matrixStats |
LinkingTo: | RcppArmadillo, Rcpp (≥ 0.11.0) |
Suggests: | irlba, testthat, knitr |
Enhances: | glmGamPoi |
Published: | 2023-10-19 |
DOI: | 10.32614/CRAN.package.sctransform |
Author: | Christoph Hafemeister [aut], Saket Choudhary [aut, cre], Rahul Satija [ctb] |
Maintainer: | Saket Choudhary <schoudhary at nygenome.org> |
BugReports: | https://github.com/satijalab/sctransform/issues |
License: | GPL-3 | file LICENSE |
URL: | https://github.com/satijalab/sctransform |
NeedsCompilation: | yes |
SystemRequirements: | C++17 |
Citation: | sctransform citation info |
Materials: | README NEWS |
CRAN checks: | sctransform results |
Reference manual: | sctransform.pdf |
Package source: | sctransform_0.4.1.tar.gz |
Windows binaries: | r-devel: sctransform_0.4.1.zip, r-release: sctransform_0.4.1.zip, r-oldrel: sctransform_0.4.1.zip |
macOS binaries: | r-release (arm64): sctransform_0.4.1.tgz, r-oldrel (arm64): sctransform_0.4.1.tgz, r-release (x86_64): sctransform_0.4.1.tgz, r-oldrel (x86_64): sctransform_0.4.1.tgz |
Old sources: | sctransform archive |
Reverse imports: | muscat, Seurat |
Reverse suggests: | CAMML, EWCE, RESET, SCdeconR, VAM |
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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.