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hashing-demultiplexing

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Assign cells to their sample of origin from cell or nucleus hashing (CITE-seq HTOs, MULTI-seq lipid/cholesterol tags, CellPlex CMOs) and call cross-sample doublets using Seurat HTODemux/MULTIseqDemux, hashsolo, demuxEM, GMM-Demux, and demuxmix. Use when assigning pooled hashed cells back to their sample, calling cross-sample doublets from HTO counts, choosing a demultiplexing method, deciding between hashtag and genetic demultiplexing, or rescuing an oversized Negative pile from weak HTO staining or ambient spillover.

When to use

• assigning pooled hashed cells back to their sample
• calling cross-sample doublets from HTO counts
• choosing a demultiplexing method
• deciding between hashtag and genetic demultiplexing
• rescuing an oversized Negative pile from weak HTO staining or ambient spillover

When not to use

• catching within-sample and homotypic doublets
• separating same-donor samples with identical genotype

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