sctransform: Variance Stabilizing Transformations for Single Cell UMI Data
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: | 0.4.2 |
| 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: | 2025-04-30 |
| DOI: | 10.32614/CRAN.package.sctransform |
| Author: | Christoph Hafemeister [aut], Saket Choudhary [aut, cre], Rahul Satija [ctb] |
| Maintainer: | Saket Choudhary <saketc at iitb.ac.in> |
| BugReports: | https://github.com/satijalab/sctransform/issues |
| License: | GPL-3 | fileLICENSE |
| URL: | https://github.com/satijalab/sctransform |
| NeedsCompilation: | yes |
| SystemRequirements: | C++17 |
| Citation: | sctransform citation info |
| Materials: | README,NEWS |
| CRAN checks: | sctransform results |
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