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bioRxiv · 10.64898/2026.08.07.743503

CellConsensus: An agent-curated atlas for automatic cell typing

de Mathelin, A.·Quinn, J. F.·Tosh, C.·TeamLab, D. S.·Tansey, W.
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Abstract

Assigning cell types to single-cell and spatial transcriptomic data remains inconsistent because marker gene knowledge is fragmented across thousands of individual studies. Here we present CellConsensus, a cell typing method built on a consensus corpus of marker genes aggregated from curated atlases (2,607 sources) and de novo mining of 1,174 papers. By reconciling overlapping and conflicting marker evidence into a consensus reference, CellConsensus assigns cell type labels that are more accurate and more reproducible than existing marker- and reference-based approaches, while remaining interpretable and applicable across tissues and platforms. CellConsensus is available as an open-source Python package (https://github.com/tansey-lab/cellconsensus), an interactive database (https://cellconsensus.org), and as an agentic MCP server for conversational querying.

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de Mathelin, A., Quinn, J. F., Tosh, C., TeamLab, D. S., Tansey, W.. 2026-08-17. CellConsensus: An agent-curated atlas for automatic cell typing. https://doi.org/10.64898/2026.08.07.743503

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