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encode-skill — Codex skill: what it does, how to install

Runs compact ENCODE REST API queries for object lookups, catalog searches, and metadata summaries. Helpful for genomic data workflows.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill encode-skill -a codex
Open on GitHub

What encode-skill does

The skill queries the ENCODE database using a local helper script named scripts/rest_request.py. It accepts a JSON payload through standard input, requesting specific accession records or catalog search results. Instead of returning raw bulk payloads, it outputs concise Markdown summaries.

Python is required to run the internal execution script. For catalog searches, the workflow uses item limits to prevent large responses. When complete API payloads are necessary, passing save_raw=true writes the full response to a designated file.

Set this up if you frequently pull metadata for assays such as RNA-seq or biosample identifiers directly into your agent session. If your work does not touch biological datasets, skip this tool.

What it helps with

  • search ENCODE experiments like RNA-seq assays
  • retrieve biosample metadata by accession identifier
  • save full raw JSON responses to local disk

Example prompts for the agent

  • Search ENCODE for the top 10 RNA-seq experiments.
  • Fetch metadata for biosample ENCBS000AAA using the ENCODE API.

How to install encode-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill encode-skill -a codex

2Manually: put the files in place

.agents/skills/encode-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about encode-skill

How to install encode-skill in Codex?

Run npx skills add openai/plugins --skill encode-skill in your project terminal.

What does encode-skill do?

It queries the ENCODE REST API via scripts/rest_request.py to retrieve compact biosample and experiment records.

Does encode-skill require external dependencies?

You only need Python to execute the bundled scripts/rest_request.py script.

See also

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