R package for modeling single cell UMI expression data using regularized negative binomial regression

This packaged was developed by Christoph Hafemeister in Rahul Satija's lab at the New York Genome Center. A previous version of this work was used in the paper Developmental diversification of cortical inhibitory interneurons, Nature 555, 2018. We are currently working on integrating the functionality of this package into Seurat, an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

This package is in beta status, please sanity check any results, and kindly notify me of any issues you find.

Quick start

devtools::install_github(repo = 'ChristophH/sctransform') normalized_data <- sctransform::vst(umi_count_matrix)$y

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sctransform documentation built on Nov. 18, 2018, 5:04 p.m.