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PreprintCC BYbioRxiv

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

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

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Cite

BibTeXRIS
BibTeX
@misc{colgan2026pycea,
  title = {{Pycea: a scverse toolkit for single-cell lineage tracing analysis}},
  author = {William N Colgan and Eric Weine and Luke W. Koblan and Matthew G Jones and Jonathan S Weissman and Nir Yosef},
  howpublished = {bioRxiv},
  year = {2026},
  month = oct,
  doi = {10.64898/2026.10.30.763227},
  url = {https://www.biorxiv.org/content/10.64898/2026.10.30.763227v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Pycea: a scverse toolkit for single-cell lineage tracing analysis
AU  - William N Colgan
AU  - Eric Weine
AU  - Luke W. Koblan
AU  - Matthew G Jones
AU  - Jonathan S Weissman
AU  - Nir Yosef
PY  - 2026
DA  - 2026/10/30
PB  - bioRxiv
DO  - 10.64898/2026.10.30.763227
UR  - https://www.biorxiv.org/content/10.64898/2026.10.30.763227v1
AB  - 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.
SN  - 2692-8205
ER  -