cellxgene-census
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.
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Install this skill
Run this command in your terminal. No account required — it auto-detects your AI tool and installs the skill file.
npx @skills-hub-ai/cli install scientific-skills-cellxgene-censusSetup by platform
Install
One-click setup for your editorRun in your project root
npx @skills-hub-ai/cli install scientific-skills-cellxgene-census --target claude-codeInstructions
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Frequently asked questions about cellxgene-census
What does the cellxgene-census skill 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. It's a reusable SKILL.md instruction set that loads into your AI coding assistant on demand, no prompt engineering, no copy-pasting every session.
How do I install the cellxgene-census skill?
Run `npx @skills-hub-ai/cli install scientific-skills-cellxgene-census` from your terminal. The CLI writes the SKILL.md to the correct location for your AI tool (e.g. ~/.claude/skills/scientific-skills-cellxgene-census/ for Claude Code or ~/.cursor/skills/ for Cursor with --target cursor) and adds it to your project's .skills.json lockfile.
Which AI tools does cellxgene-census work with?
cellxgene-census runs in Claude Code. It follows the open Agent Skills standard (SKILL.md), so the same skill works in every supported tool without modification.
Is the cellxgene-census skill free?
Yes. Every skill on skills-hub.ai is free and open-source. There are no premium tiers, paywalls, or usage limits. You only pay for whatever AI assistant you're already using.
How do I use cellxgene-census after installing it?
In Claude Code, type `/scientific-skills-cellxgene-census` (or whatever slash command the skill registers) and the AI follows the skill's instructions immediately. You can also reference it by name in natural language, your AI loads the skill into context when relevant.
Can I share the cellxgene-census skill with my team?
Yes. Commit your project's .skills.json lockfile and teammates run `npx @skills-hub-ai/cli install` (no args) to install every skill at the exact version you pinned. Organization-scoped installs work via skills-hub.ai organizations.