doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9> for more details.">

sctransform: Variance Stabilizing Transformations for Single Cell UMI Data (original) (raw)

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 HafemeisterORCID iD [aut], Saket Choudhary ORCID iD [aut, cre], Rahul Satija ORCID iD [ctb]
Maintainer: Saket Choudhary
BugReports: https://github.com/satijalab/sctransform/issues
License: GPL-3 | file
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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