Cellxgene Skill for Codex

Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries

3k tokens

context cost

the whole folder, loaded on every use

files

ships runnable scripts

copies elsewhere

how many repositories repackaged it

4915

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/openai/plugins --skill cellxgene-skill

What comes with it

10 827 bytes besides the instruction

agents/openai.yaml

scripts/rest_request.py

The instruction itself

6 sections, as written by the author

Operating rules

Use scripts/rest_request.py for all CELLxGENE Discover calls.
Use base_url=https://api.cellxgene.cziscience.com/curation/v1.
Prefer targeted collection detail lookups rather than full archive dumps by default.
The public collections list can be large and may require a higher timeout_sec; collection detail lookups are usually the better first call.
Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

Return concise markdown summaries from the script JSON by default.
Return raw JSON only if the user explicitly asks for machine-readable output.
Prefer these paths: collections/<collection_id> first, then collections when the user explicitly wants broad archive discovery.

Input

Read one JSON object from stdin.
Required fields: base_url, path
Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
Common CELLxGENE patterns:
{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}
{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections","timeout_sec":60,"max_items":5}

Output

Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}' | python scripts/rest_request.py

References

No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.

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27k tokens scripts

How to use it

Copy the folder

Take openai/cellxgene-skill from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.