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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 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++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:

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.