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Cellxgene Census

Cellxgene Census is an agent skill (a SKILL.md file) from K-Dense-AI/scientific-agent-skills. It queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. It works with Claude Code, Codex, Cursor, Gemini CLI and GitHub Copilot and has 54,643 GitHub stars across a repository of 7 listed skills.

github.com/K-Dense-AI/scientific-agent-skills/skills/cellxgene-census (opens in a new tab)

Data as of from the GitHub API; description from the skill's SKILL.md. Report an error

View on GitHub (opens in a new tab)

Add this skill

Claude

Claude Code loads skills from ~/.claude/skills/ (all projects) or .claude/skills/ (one project):

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/cellxgene-census ~/.claude/skills/cellxgene-census   # personal, or .claude/skills in a project

In the Claude apps, zip the cellxgene-census folder and upload it under Customize > Skills > + > Upload a skill (code execution must be on).

ChatGPT / Codex

Codex reads skills from .agents/skills/ in a repo or ~/.agents/skills/ for every project:

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/cellxgene-census .agents/skills/cellxgene-census   # repo; ~/.agents/skills for all projects

Standalone skills also load in the ChatGPT desktop app.

Cursor

Cursor loads skills from .cursor/skills/ (or ~/.cursor/skills/) and also reads .claude/skills/:

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/cellxgene-census .cursor/skills/cellxgene-census   # project; ~/.cursor/skills for all projects

Source (checked Oct 7, 2026): code.claude.com/docs/en/skills (opens in a new tab), support.claude.com/en/articles/12512180-using-skills-in-claude (opens in a new tab), learn.chatgpt.com/docs/build-skills (opens in a new tab), cursor.com/docs/context/skills (opens in a new tab)

What this skill does

Queries 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.

When it triggers

  • 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 ce

More skills in K-Dense-AI/scientific-agent-skills

7 skills are listed from this repository.

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FAQ

Cellxgene Census FAQ

Still curious? Email info@appsgit.com.

How do I install the Cellxgene Census skill?

Copy the cellxgene-census folder (the one containing SKILL.md) into ~/.claude/skills/ for Claude Code, .agents/skills/ for Codex or .cursor/skills/ for Cursor. The agent picks it up automatically when a task matches its description.

Is the Cellxgene Census skill free?

Yes. The repository is open source under the MIT license.

Is Cellxgene Census maintained?

The repository's most recent commit was on Oct 19, 2026. Its latest release is v2.72.0. appsgit only lists skills from repositories with a commit in the last six months.