Pycea: a scverse toolkit for single-cell lineage tracing analysis

Pycea is an open-source Python toolkit that integrates lineage tree analysis with single-cell measurements via TreeData, enabling scalable visualization, clade finding, and ancestral inference.

• Why it matters: Lineage tracing can reveal cellular histories, but combining lineage data with single-cell workflows is difficult, especially when moving between analysis formats.
• What they did: The authors built TreeData as an AnnData extension to store lineage trees alongside cellular measurements, compatible with Scanpy and other scverse tools. Pycea adds scalable methods for visualization, clade identification, distance comparisons, ancestral state inference, and lineage statistics.
• The result: The toolkit supports integrated lineage-and-single-cell analysis without converting between formats, facilitating end-to-end reconstruction and quantitative lineage characterization.

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