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Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods.

ABSTRACT: Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences. An implicit challenge with scRNA-seq is the occurrence of doublets-droplets containing two or more cells. We develop Demuxafy, a framework to enhance donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. Demuxafy significantly improves droplet assignment by separating singlets from doublets and classifying the correct individual.

SUBMITTER: Neavin D

PROVIDER: S-EPMC11020463 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature

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Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods.

Neavin Drew D Senabouth Anne A Arora Himanshi H Lee Jimmy Tsz Hang JTH Ripoll-Cladellas Aida A Franke Lude L Prabhakar Shyam S Ye Chun Jimmie CJ McCarthy Davis J DJ Melé Marta M Hemberg Martin M Powell Joseph E JE

Genome biology 20240415 1

Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences. An implicit challenge with scRNA-seq is the occurrence of doublets-droplets containing two or more cells. We develop Demuxafy, a framework to enhance donor assignment an ...[more]

PMID: 38622708

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