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:10.1101/576827> for more details.

Version: 0.2.0
Depends: R (≥ 3.0.2)
Imports: MASS, Matrix, methods, future, future.apply, ggplot2, reshape2, gridExtra, Rcpp
LinkingTo: Rcpp (≥ 0.11.0), RcppEigen
Suggests: irlba, testthat
Published: 2019-04-12
Author: Christoph Hafemeister ORCID iD [aut, cre]
Maintainer: Christoph Hafemeister <chafemeister at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
Materials: README
CRAN checks: sctransform results


Reference manual: sctransform.pdf
Package source: sctransform_0.2.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X binaries: r-release: sctransform_0.2.0.tgz, r-oldrel: sctransform_0.1.0.tgz
Old sources: sctransform archive

Reverse dependencies:

Reverse imports: Seurat


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