Cellxgene Census
This gives you direct access to 61+ million standardized single-cell genomics records from the CZ CELLxGENE Census. You can filter by cell type, tissue, or disease, then pull expression matrices into scanpy for analysis or pipe them into PyTorch dataloaders for training ML models. The API handles both in-memory queries for smaller datasets and streaming iterators when you're working with millions of cells that won't fit in RAM. It's built on top of SOMA, so you get versioned snapshots for reproducibility. If you're doing population-scale single-cell work or need large labeled datasets for cell type classification, this beats scraping individual studies from GEO.
- skills.sh installs
- 219
- GitHub stars
- 33.2K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add davila7/claude-code-templates --skill cellxgene-census --agent claude-codeInstalls into .claude/skills of the current project.
Files
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
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:
uv pip install cellxgene-census
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- Repository
- github.com/davila7/claude-code-templates
- Category
- Data Science & ML
- First seen
- Jun 3, 2026
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