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

Lineage tracing enables reconstruction of cellular histories in development, regeneration, and disease, but integrating lineage data into single-cell analysis workflows remains challenging. We introduce Pycea, a Python toolkit for lineage analysis and visualization, and TreeData, an extension of AnnData that stores lineage trees alongside cellular measurements. TreeData is compatible with Scanpy and other scverse tools, enabling integrated analysis without converting between formats. Pycea provides scalable methods for tree visualization, clade identification, distance comparisons, ancestral state inference, and lineage statistics. This software is open source and available at https://github.com/YosefLab/pycea.