CZ CELLxGENE Census
Overview
The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first.
The Census includes:
- 217+ million total cells and 125+ million unique cells in the 2025-11-08 stable LTS release
- 1,845 datasets in the 2025-11-08 stable LTS release
- Human, mouse, marmoset, rhesus macaque, and chimpanzee data in the current schema
- Standardized metadata (cell types, tissues, diseases, donors)
- Raw gene expression matrices and source H5AD lookup/download helpers
- Pre-calculated summary counts, embeddings, and spatial data
- Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools
When to Use This Skill
This skill should be used when:
- Querying single-cell expression data by cell type, tissue, or disease
- Exploring available single-cell datasets and metadata
- Training machine learning models on single-cell data
- Performing large-scale cross-dataset analyse…
