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 | file LICENSE URL: https://github.com/satijalab/sctransform NeedsCompilation: yes SystemRequirements: C++17 Citation: sctransform citation info Materials: README NEWS CRAN checks: sctransform results Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=sctransform to link to this page.
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