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...
| Main Authors: | , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/179610 |
| _version_ | 1811688614304677888 |
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| author | Neavin, Drew Senabouth, Anne Arora, Himanshi Lee, Jimmy Tsz Hang Ripoll-Cladellas, Aida Franke, Lude Prabhakar, Shyam Ye, Jimmie Chun McCarthy, Davis J. Melé, Marta Hemberg, Martin Powell, Joseph E. |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) Neavin, Drew Senabouth, Anne Arora, Himanshi Lee, Jimmy Tsz Hang Ripoll-Cladellas, Aida Franke, Lude Prabhakar, Shyam Ye, Jimmie Chun McCarthy, Davis J. Melé, Marta Hemberg, Martin Powell, Joseph E. |
| author_sort | Neavin, Drew |
| collection | NTU |
| description | 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 | 2024-10-01T05:35:00Z |
| format | Journal Article |
| id | ntu-10356/179610 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:35:00Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1796102024-08-18T15:39:32Z Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods Neavin, Drew Senabouth, Anne Arora, Himanshi Lee, Jimmy Tsz Hang Ripoll-Cladellas, Aida Franke, Lude Prabhakar, Shyam Ye, Jimmie Chun McCarthy, Davis J. Melé, Marta Hemberg, Martin Powell, Joseph E. Lee Kong Chian School of Medicine (LKCMedicine) Genome Institute of Singapore, A*STAR Cancer Science Institute of Singapore, NUS Medicine, Health and Life Sciences Single-cell analysis Genetic demultiplexing 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. Published version This work was funded by the National Health and Medical Research Council (NHMRC) Investigator grant (1175781), and funding from the Goodridge foundation. J.E.P is also supported by a fellowship from the Fok Foundation. 2024-08-13T02:16:50Z 2024-08-13T02:16:50Z 2024 Journal Article Neavin, D., Senabouth, A., Arora, H., Lee, J. T. H., Ripoll-Cladellas, A., Franke, L., Prabhakar, S., Ye, J. C., McCarthy, D. J., Melé, M., Hemberg, M. & Powell, J. E. (2024). Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods. Genome Biology, 25(1). https://dx.doi.org/10.1186/s13059-024-03224-8 1474-760X https://hdl.handle.net/10356/179610 10.1186/s13059-024-03224-8 25 2-s2.0-85190420802 1 25 en Genome Biology © The Author(s) 2024. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the mate rial. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdo main/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Single-cell analysis Genetic demultiplexing Neavin, Drew Senabouth, Anne Arora, Himanshi Lee, Jimmy Tsz Hang Ripoll-Cladellas, Aida Franke, Lude Prabhakar, Shyam Ye, Jimmie Chun McCarthy, Davis J. Melé, Marta Hemberg, Martin Powell, Joseph E. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods |
| 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 | Medicine, Health and Life Sciences Single-cell analysis Genetic demultiplexing |
| url | https://hdl.handle.net/10356/179610 |
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