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

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...

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Bibliographic Details
Published in:Genome Biology 2024-04, Vol.25 (1), p.94-94, Article 94
Main Authors: Neavin, Drew, Senabouth, Anne, Arora, Himanshi, Lee, Jimmy Tsz Hang, Ripoll-Cladellas, Aida, Franke, Lude, Prabhakar, Shyam, Ye, Chun Jimmie, McCarthy, Davis J, Melé, Marta, Hemberg, Martin, Powell, Joseph E
Format: Article
Language:English
Subjects:
Datasets
Doublet detecting
droplets
Fibroblasts
Genetic demultiplexing
genome
Humans
Method
Methods
sequence analysis
Sequence Analysis, RNA - methods
Single-cell analysis
Single-Cell Analysis - methods
Software
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Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-024-03224-8