cellxgene-census

SUMMARY

What it does

This Agent Skill provides procedural knowledge for querying the CZ CELLxGENE Census programmatically. It enables access to versioned public single-cell and spatial transcriptomics data, including population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, and reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. The skill includes installation instructions, core workflow patterns, best practices, and troubleshooting guidance. It is designed for use with Python >=3.10,<3.13 and targets cellxgene-census 1.17.x and the 2025-11-08 stable LTS Census. No authentication is required for public Census data.