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cellxgene-census

Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

cli-tool/components/skills/scientific/cellxgene-census/SKILL.md

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# CZ CELLxGENE Census

## Overview

The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell genomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of millions of cells across thousands of datasets.

The Census includes:
- **61+ million cells** from human and mouse
- **Standardized metadata** (cell types, tissues, diseases, donors)
- **Raw gene expression** matrices
- **Pre-calculated embeddings** and statistics
- **Integration with PyTorch, scanpy, and other analysis tools**

## When to Use This Skill