cellxgene-census
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
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