Version Compatibility

Reference examples tested with: Cassiopeia 2.0+, CoSpar 0.3+, scanpy 1.10+, numpy 1.26+

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

• Python: pip show <package> then help(module.function) to check signatures

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

Lineage Tracing

"Reconstruct cell lineage from barcodes" -> Read heritable marks across single cells and ask which cells share which marks to recover an ontogenetic phylogeny or clonal grouping.

• Python: cassiopeia (scar-tree reconstruction), cospar (clone + state integration), mtDNA variant callers (mgatk/MAESTER pipelines)

Governing Principle

Transcriptomic state does NOT fully predict fate. Weinreb 2020 (LARRY) showed sister cells in an indistinguishable transcriptomic state systematically diverge in fate, so the information that decides a bifurcation is heritable but invisible to the measured transcriptome. Three consequences drive every decision here.