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 leverag...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-04-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-024-03224-8 |
| _version_ | 1827277101994082304 |
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| author | Drew Neavin Anne Senabouth Himanshi Arora Jimmy Tsz Hang Lee Aida Ripoll-Cladellas sc-eQTLGen Consortium Lude Franke Shyam Prabhakar Chun Jimmie Ye Davis J. McCarthy Marta Melé Martin Hemberg Joseph E. Powell |
| author_facet | Drew Neavin Anne Senabouth Himanshi Arora Jimmy Tsz Hang Lee Aida Ripoll-Cladellas sc-eQTLGen Consortium Lude Franke Shyam Prabhakar Chun Jimmie Ye Davis J. McCarthy Marta Melé Martin Hemberg Joseph E. Powell |
| author_sort | Drew Neavin |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-24T07:15:13Z |
| format | Article |
| id | doaj.art-7209fadf8e984cfb87325f01f83f0d88 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-24T07:15:13Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-7209fadf8e984cfb87325f01f83f0d882024-04-21T11:20:37ZengBMCGenome Biology1474-760X2024-04-0125112410.1186/s13059-024-03224-8Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methodsDrew Neavin0Anne Senabouth1Himanshi Arora2Jimmy Tsz Hang Lee3Aida Ripoll-Cladellas4sc-eQTLGen ConsortiumLude Franke5Shyam Prabhakar6Chun Jimmie Ye7Davis J. McCarthy8Marta Melé9Martin Hemberg10Joseph E. Powell11Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical ResearchGarvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical ResearchGarvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical ResearchWellcome Sanger Institute, Wellcome Genome CampusLife Sciences DepartmentDepartment of Genetics, University of Groningen, University Medical Center GroningenSpatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)Bakar Institute for Computational Health Sciences, University of CaliforniaBioinformatics and Cellular Genomics, St Vincent’s Institute of Medical ResearchLife Sciences DepartmentPresent address: The Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital and Harvard Medical SchoolGarvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical ResearchAbstract 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.https://doi.org/10.1186/s13059-024-03224-8Single-cell analysisGenetic demultiplexingDoublet detecting |
| spellingShingle | Drew Neavin Anne Senabouth Himanshi Arora Jimmy Tsz Hang Lee Aida Ripoll-Cladellas sc-eQTLGen Consortium Lude Franke Shyam Prabhakar Chun Jimmie Ye Davis J. McCarthy Marta Melé Martin Hemberg Joseph E. Powell Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods Genome Biology Single-cell analysis Genetic demultiplexing Doublet detecting |
| title | Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| title_full | Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| title_fullStr | Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| title_full_unstemmed | Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| title_short | Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| title_sort | demuxafy improvement in droplet assignment by integrating multiple single cell demultiplexing and doublet detection methods |
| topic | Single-cell analysis Genetic demultiplexing Doublet detecting |
| url | https://doi.org/10.1186/s13059-024-03224-8 |
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