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 for interrogating the transcriptomes of single cells on a large scale. Pooling and processing cells from different samples together can reduce costs and batch effects. To pool cells, they are often first labeled with hashtag oligonucleotides (HTOs). These HTOs are sequenced alongside the cells' RNA in the droplets and subsequently used to computationally assign each droplet to its sample of origin, a process referred to as demultiplexing. Accurate demultiplexing is crucial but can be challenging due to background HTOs, low-quality cells/cell debris, and multiplets.

Results

A new demultiplexing method based on negative binomial regression mixture models is introduced. The met

SUBMITTER: Klein HU 

PROVIDER: S-EPMC10412409 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature