hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse sa...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
BioMed Central
2024
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| _version_ | 1817930900094058496 |
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| author | Curion, F Wu, X Heumos, L André, MMG Halle, L Ozols, M Grant-Peters, M Rich-Griffin, C Yeung, H Dendrou, CA Schiller, HB Theis, FJ |
| author_facet | Curion, F Wu, X Heumos, L André, MMG Halle, L Ozols, M Grant-Peters, M Rich-Griffin, C Yeung, H Dendrou, CA Schiller, HB Theis, FJ |
| author_sort | Curion, F |
| collection | OXFORD |
| description | Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. |
| first_indexed | 2024-09-25T04:14:55Z |
| format | Journal article |
| id | oxford-uuid:1484b977-775d-459f-bb6d-d0a939587448 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:13:28Z |
| publishDate | 2024 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:1484b977-775d-459f-bb6d-d0a9395874482024-10-16T09:19:06Zhadge: a comprehensive pipeline for donor deconvolution in single-cell studiesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:1484b977-775d-459f-bb6d-d0a939587448EnglishJisc Publications RouterBioMed Central2024Curion, FWu, XHeumos, LAndré, MMGHalle, LOzols, MGrant-Peters, MRich-Griffin, CYeung, HDendrou, CASchiller, HBTheis, FJSingle-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. |
| spellingShingle | Curion, F Wu, X Heumos, L André, MMG Halle, L Ozols, M Grant-Peters, M Rich-Griffin, C Yeung, H Dendrou, CA Schiller, HB Theis, FJ hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title_full | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title_fullStr | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title_full_unstemmed | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title_short | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| title_sort | hadge a comprehensive pipeline for donor deconvolution in single cell studies |
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