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> for more details.

Version: 0.3.2
Depends: R (≥ 3.1.0)
Imports: MASS, Matrix, methods, future.apply, future, ggplot2, reshape2, gridExtra, matrixStats
LinkingTo: RcppArmadillo, Rcpp (≥ 0.11.0)
Suggests: irlba, testthat, knitr
Enhances: glmGamPoi
Published: 2020-12-16
Author: Christoph Hafemeister ORCID iD [aut, cre]
Maintainer: Christoph Hafemeister <christoph.hafemeister at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
SystemRequirements: C++11
Citation: sctransform citation info
Materials: README NEWS
CRAN checks: sctransform results


Reference manual: sctransform.pdf


Package source: sctransform_0.3.2.tar.gz
Windows binaries: r-devel:, r-devel-UCRT:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): sctransform_0.3.2.tgz, r-release (x86_64): sctransform_0.3.2.tgz, r-oldrel: sctransform_0.3.2.tgz
Old sources: sctransform archive

Reverse dependencies:

Reverse imports: muscat, Seurat
Reverse suggests: EWCE, mistyR, VAM


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