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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill cellxgene-census --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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: ```bash uv pip install cellxgene-census ``` For machine learning workflows, install additional dependencie
- Overview
- When to Use This Skill
- Installation and Setup
- Core Workflow Patterns
- 1. Opening the Census
- 2. Exploring Census Information
- 3. Querying Expression Data (Small to Medium Scale)
- 4. Large-Scale Queries (Out-of-Core Processing)
- 5. Machine Learning with PyTorch
- 6. Integration with Scanpy
- 7. Multi-Dataset Integration
- Key Concepts and Best Practices
- Always Filter for Primary Data
- Specify Census Version for Reproducibility
uv pip install cellxgene-census uv pip install cellxgene-census[experimental]
What does the cellxgene-census skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill cellxgene-census --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.