R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
This packaged was developed by Christoph Hafemeister in Rahul Satija's lab at the New York Genome Center. Core functionality of this package has been integrated into Seurat, an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
devtools::install_github(repo = 'ChristophH/sctransform')
normalized_data <- sctransform::vst(umi_count_matrix)$y
For usage examples see vignettes in inst/doc or use the built-in help after installation
An early version of this work was used in the paper Developmental diversification of cortical inhibitory interneurons, Nature 555, 2018.