name: kdense-cellxgene-census description: "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." metadata: version: "1.0.1"

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Kdense Cellxgene Census

Use this Codex adapter for the pinned upstream scientific skill.

Catalog status

• Status: active
• Source: kdense
• Audit reasons: none
• Upstream license: MIT
• Inventory: ../../inventory.json
• Upstream instructions: ../../../vendor/scientific-agent-skills/skills/cellxgene-census/SKILL.md

Procedure

1. Resolve the plugin root as three directories above this skill directory.
2. Run "<plugin-root>/scripts/python_runtime.sh" "<plugin-root>/scripts/search_skills.py" --name kdense-cellxgene-census and verify the record's status, reasons, and source path and the source's pinned commit (empty for first-party cx skills) from its output instead of reading inventory.json.
3. Read the upstream instructions only after confirming this record is still active in the current inventory.
4. Treat upstream frontmatter as source metadata, not as Codex configuration. Follow the instruction body only where it is compatible with available Codex tools and the current user-approved plan.
5. Treat tools named for another agent runtime as capability requests. Map them to an available Codex tool only when the behavior is equivalent; otherwise report the unavailable capability.
6. Ask before credentials, package installation, new network hosts, remote compute, writes, paid services, destructive actions, or imported executable code.
7. Use $science-provenance for produced scientific outputs and $science-review before presenting scientific claims.

Progressive loading

The upstream SKILL.md is 559 lines. Inspect its headings first, then read only the sections relevant to the current request. Load linked references only when the selected workflow requires them; do not load the entire upstream tree by default.

Boundaries

• This wrapper does not grant credentials, network access, package installation, or script execution.
• Do not change an inactive record to active from inside a research task.
• Preserve failures, uncertainty, source identifiers, and licensing constraints.