CRAN: Package sctransform

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: 0.4.2

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: 2025年04月30日

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 <saketc at iitb.ac.in>

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.html , sctransform.pdf

Downloads:

Package source: sctransform_0.4.2.tar.gz

Windows binaries: r-devel: sctransform_0.4.2.zip, r-release: sctransform_0.4.2.zip, r-oldrel: sctransform_0.4.2.zip

macOS binaries: r-release (arm64): sctransform_0.4.2.tgz, r-oldrel (arm64): sctransform_0.4.2.tgz, r-release (x86_64): sctransform_0.4.2.tgz, r-oldrel (x86_64): sctransform_0.4.2.tgz

Old sources: sctransform archive

Reverse dependencies:

Reverse imports: muscat, Seurat, spatialGE

Reverse suggests: CAMML, EWCE, RESET, SCdeconR, VAM

Linking:

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