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Curion, F. ; Wu, X. ; Heumos, L. ; Gonzales André, M.M. ; Halle, L. ; Ozols, M.* ; Grant-Peters, M.* ; Rich-Griffin, C.* ; Yeung, H.Y.* ; Dendrou, C.A.* ; Schiller, H. ; Theis, F.J.

hadge: A comprehensive pipeline for donor deconvolution in single-cell studies.

Genome Biol. 25:109 (2024)
DOI PMC
Creative Commons Lizenzvertrag
Open Access Gold as soon as Publ. Version/Full Text is submitted to ZB.
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.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Donor Deconvolution ; Genetic ; Hashing ; Nextflow ; Single-cell; Rna-seq
ISSN (print) / ISBN 1474-760X
e-ISSN 1465-6906
Journal Genome Biology
Quellenangaben Volume: 25, Issue: 1, Pages: , Article Number: 109 Supplement: ,
Publisher BioMed Central
Publishing Place Campus, 4 Crinan St, London N1 9xw, England
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Lung Health and Immunity (LHI)
Grants Helmholtz Zentrum Mnchen - Deutsches Forschungszentrum fr Gesundheit und Umwelt (GmbH) (4209)