cellxgene-census-query

What problem does it solve?

Enables programmatic access to CZ CELLxGENE Census data for scalable, reproducible single-cell analyses by filtering datasets and retrieving expression data and metadata without downloading entire files.

Core Features & Use Cases

• Programmatic querying by cell type, tissue, disease, and dataset version
• Retrieval of expression data, metadata, embeddings, and statistics
• Integration with PyTorch, Scanpy, and other analysis tools for ML and bioinformatics workflows
• Cross-dataset analyses and out-of-core processing for large population-scale datasets

Quick Start

Open a Soma session and run a minimal query to fetch an AnnData object for a tissue of interest