CZ CELLxGENE Census

Overview

CZ CELLxGENE Census provides programmatic access to 61+ million standardized single-cell RNA-seq observations from human and mouse. It enables population-scale queries by cell type, tissue, disease, and donor metadata, returning expression data as AnnData objects or PyTorch dataloaders for ML workflows.

When to Use

• Querying single-cell expression data across tissues, diseases, or cell types from a curated atlas
• Building reference datasets for cell type classification or marker gene discovery
• Training ML models on large-scale single-cell data (PyTorch integration)
• Comparing gene expression across conditions (e.g., COVID-19 vs healthy) at population scale
• Exploring what single-cell datasets are available for a tissue or disease of interest
• For analyzing your own scRNA-seq data, use scanpy instead
• For manipulating AnnData objects (subsetting, concatenation), use anndata instead

Prerequisites