cellxgene-census

# 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 analyses - Integrating Census data with scanpy or other analysis frameworks - Computing statistics across millions of cells - Accessing pre-calculated embeddings or model predictions ## Installation and Setup Install the Census API: ```bash uv pip install "cellxgene-census==1.17.*" ``` For spatial workf...