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 (2022) <doi:10.1186/s13059-021-02584-9> for more details.

Version:	0.4.1
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:	2023-10-19
DOI:	10.32614/CRAN.package.sctransform
Author:	Christoph Hafemeister [aut], Saket Choudhary [aut, cre], Rahul Satija [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++17
Citation:	sctransform citation info
Materials:	README NEWS
CRAN checks:	sctransform results

Documentation:

Reference manual:

sctransform.pdf

Downloads:

Package source:	sctransform_0.4.1.tar.gz
Windows binaries:	r-devel: sctransform_0.4.1.zip, r-release: sctransform_0.4.1.zip, r-oldrel: sctransform_0.4.1.zip
macOS binaries:	r-release (arm64): sctransform_0.4.1.tgz, r-oldrel (arm64): sctransform_0.4.1.tgz, r-release (x86_64): sctransform_0.4.1.tgz, r-oldrel (x86_64): sctransform_0.4.1.tgz
Old sources:	sctransform archive

Reverse dependencies:

Reverse imports:	muscat, Seurat
Reverse suggests:	CAMML, EWCE, RESET, SCdeconR, VAM

Linking:

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