Work

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

Year: 2026

Type: preprint

Abstract: 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.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.10.30.763227

Authors: William N Colgan, Eric Weine, Luke W. Koblan, Matthew G Jones, Jonathan S Weissman, Nir Yosef

Institutions: Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Weizmann Institute of Science

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Howard Hughes Medical Institute, Helen Hay Whitney Foundation, Chan Zuckerberg Initiative, National Institutes of Health

OpenAlex ID: W7225043067

Cites: 43

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Related to: 10