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> for more details.

Version: 0.3.1
Depends: R (≥ 3.1.0)
Imports: MASS, Matrix, methods, future.apply, future, ggplot2, reshape2, gridExtra, matrixStats
LinkingTo: RcppArmadillo, Rcpp (≥ 0.11.0)
Suggests: irlba, testthat, knitr
Enhances: glmGamPoi
Published: 2020-10-08
Author: Christoph Hafemeister ORCID iD [aut, cre]
Maintainer: Christoph Hafemeister <christoph.hafemeister at nyu.edu>
BugReports: https://github.com/ChristophH/sctransform/issues
License: GPL-3 | file LICENSE
URL: https://github.com/ChristophH/sctransform
NeedsCompilation: yes
SystemRequirements: C++11
Citation: sctransform citation info
Materials: README NEWS
CRAN checks: sctransform results

Downloads:

Reference manual: sctransform.pdf
Package source: sctransform_0.3.1.tar.gz
Windows binaries: r-devel: sctransform_0.3.1.zip, r-release: sctransform_0.3.1.zip, r-oldrel: sctransform_0.3.1.zip
macOS binaries: r-release: sctransform_0.3.1.tgz, r-oldrel: sctransform_0.3.1.tgz
Old sources: sctransform archive

Reverse dependencies:

Reverse imports: muscat, Seurat

Linking:

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