Overview
cellxgene-census is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source…”. The project has 45k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cellxgene-census`.
What cellxgene-census does
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.
What’s inside
The SKILL.md for cellxgene-census is organised into these sections:
- Overview
- When to Use This Skill
- Installation and Setup
- Core Workflow Patterns
- Key Concepts and Best Practices
- Always Filter for Primary Data
- Specify Census Version for Reproducibility
- Estimate Query Size Before Loading
- Use tissuegeneral for Broader Groupings
- Select Only Needed Columns
- Check Dataset Presence for Gene-Specific Queries
- Two-Step Workflow: Explore Then Query
Installation
Add cellxgene-census to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cellxgene-censusReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
cellxgene-census is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 44,861 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 11,040 GitHub stars over the last 27 days
Author
Topics
Frequently asked questions
- What does cellxgene-census do?
- Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
- How do I install cellxgene-census?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/cellxgene-census in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is cellxgene-census free to use?
- Yes. cellxgene-census is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does cellxgene-census come from?
- cellxgene-census ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 44,861 GitHub stars apply to that whole collection, not to this skill on its own.