Cellxgene Census
This gives you programmatic access to 61+ million standardized single cells from the CELLxGENE Census, the largest curated single-cell atlas available. You can query expression data by cell type, tissue, or disease across thousands of datasets without downloading everything. The API handles both small queries that fit in memory with get_anndata() and massive out-of-core processing with iterative batching. It integrates cleanly with scanpy for standard analysis workflows and includes PyTorch dataloaders for training models on cell data. Worth noting that you should always filter for is_primary_data to avoid counting duplicate cells. If you're analyzing your own data rather than querying reference atlases, stick with scanpy or scvi-tools instead.
- skills.sh installs
- 2K
- GitHub stars
- 56.6K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add k-dense-ai/scientific-agent-skills --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 and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first.
The Census includes:
- 217+ million total cells and 125+ million unique cells in the 2025-11-08 stable LTS release
- 1,845 datasets in the 2025-11-08 stable LTS release
- Human, mouse, marmoset, rhesus macaque, and chimpanzee data in the current schema
- Standardized metadata (cell types, tissues, diseases, donors)
- Raw gene expression matrices and source H5AD lookup/download helpers
- Pre-calculated summary counts, embeddings, and spatial data
- Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools
When to Use This Skill
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- Repository
- github.com/k-dense-ai/scientific-agent-skills
- Category
- AI & Agent Building
- First seen
- Jun 3, 2026
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