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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.

Original publication

DOI

10.1186/s13059-024-03249-z

Type

Journal article

Journal

Genome biology

Publication Date

04/2024

Volume

25

Addresses

Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany.

Keywords

Brain, Humans, Genotype, Software, Single-Cell Analysis