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 (2021) <doi:10.1101/2021.07.07.451498> for more details.

Version: 0.3.3
Depends: R (≥ 3.5.0)
Imports: dplyr, magrittr, MASS, Matrix, methods, future.apply, future, ggplot2, reshape2, rlang, gridExtra, matrixStats
LinkingTo: RcppArmadillo, Rcpp (≥ 0.11.0)
Suggests: irlba, testthat, knitr
Enhances: glmGamPoi
Published: 2022-01-13
Author: Christoph Hafemeister ORCID iD [aut], Saket Choudhary ORCID iD [aut, cre], Rahul Satija ORCID iD [ctb]
Maintainer: Saket Choudhary <schoudhary at nygenome.org>
BugReports: https://github.com/satijalab/sctransform/issues
License: GPL-3 | file LICENSE
URL: https://github.com/satijalab/sctransform
NeedsCompilation: yes
SystemRequirements: C++11
Citation: sctransform citation info
Materials: README NEWS
CRAN checks: sctransform results

Documentation:

Reference manual: sctransform.pdf

Downloads:

Package source: sctransform_0.3.3.tar.gz
Windows binaries: r-devel: sctransform_0.3.3.zip, r-devel-UCRT: sctransform_0.3.3.zip, r-release: sctransform_0.3.3.zip, r-oldrel: sctransform_0.3.3.zip
macOS binaries: r-release (arm64): sctransform_0.3.3.tgz, r-release (x86_64): sctransform_0.3.3.tgz, r-oldrel: sctransform_0.3.2.tgz
Old sources: sctransform archive

Reverse dependencies:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=sctransform to link to this page.