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.

Getting started

Package details

AuthorChristoph Hafemeister [aut] (<https://orcid.org/0000-0001-6365-8254>), Saket Choudhary [aut, cre] (<https://orcid.org/0000-0001-5202-7633>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
MaintainerSaket Choudhary <schoudhary@nygenome.org>
LicenseGPL-3 | file LICENSE
Version0.3.5
URL https://github.com/satijalab/sctransform
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("sctransform")

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sctransform documentation built on Sept. 22, 2022, 1:09 a.m.