Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers

About

The purpose of this package is to remove PCR distortion from scRNA-seq read counts by normalizing to quasi-UMI counts (QUMIs). QUMIs approximate the true (unmeasured) UMI counts. Once read counts or TPM are transformed to QUMIs, the count matrix can be passed to UMI-specific methods for feature selection and dimension reduction, such as those provided in the scry package.

For more details see the Genome Biology paper. Please cite the publication if you use this package in your research. If you find bugs please create a github issue.

See the DESCRIPTION file for a list of authors and contributors.

Installation

remotes::install_github("willtownes/quminorm")

Usage

Please refer to the vignettes.