Version Compatibility

Reference examples tested with: Seurat 5.0+, scanpy 1.10+, pegasus 1.8+, demuxmix 1.4+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Hashtag Demultiplexing and Cross-Sample Doublet Calling

"Which sample did each cell come from, and which barcodes are cross-sample doublets?" -> Classify every cell's HTO count vector to the one tag that dominates its background, and flag cells where two tags are both high.

• R: Seurat::HTODemux (antibody HTOs), Seurat::MULTIseqDemux (MULTI-seq lipid tags), demuxmix (regression mixture, robust to bad staining)
• Python: scanpy.external.pp.hashsolo (Bayesian), pegasus.demultiplex / demuxEM (background from empty droplets)
• CLI: GMM-Demux (Gaussian mixture with explicit multiplet accounting)

Governing principle