Demuxmix: Demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models.

ABSTRACT:

Motivation

Droplet-based single-cell RNA sequencing (scRNA-seq) is widely used in biomedical research to interrogate the transcriptomes of single cells on a large scale. Pooling and processing cells from different samples together can reduce costs and batch effects. In order to pool cells, cells are often first labeled with hashtag oligonucleotides (HTOs). These HTOs are sequenced along with the cells' RNA in the droplets and are subsequently used to computationally assign each droplet to its sample of origin, which is referred to as demultiplexing. Accurate demultiplexing is crucial and can be challenging due to background HTOs, low-quality cells/cell debris, and multiplets.

Results

A new demultiplexing method, demuxmix, based on negative binomial regression mixture models

SUBMITTER: Klein HU 

PROVIDER: S-EPMC9901175 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature