sctransform

CRANsctransformMaRDI QIDQ88874

Variance Stabilizing Transformations for Single Cell UMI Data

Christoph Hafemeister, Saket Choudhary

Last update: 19 October 2023

Software version identifier: 0.3.5, 0.1.0, 0.2.0, 0.2.1, 0.3.1, 0.3.2, 0.3.3, 0.3.4, 0.3, 0.4.0, 0.4.1

Copyright license: GNU General Public License, version 3.0, File License

Description

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.

Cites work

• Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
• Comparison and evaluation of statistical error models for scRNA-seq