/search-encode
Search ENCODE experiments by assay, organ, biosample, or target
$ npx -y skills add ammawla/encode-toolkit --agent claude-codeShips with encode-toolkit. Installing the plugin gets this command.
How it fires
How this command gets triggered: by you, by Claude, or both.
- Fires itselfClaude auto-loads it when your prompt matches the work.
- You can call itInvoke it directly when you want it.
- Slash command
/search-encode
Context preview
What this command does when you run it.
Search ENCODE experiments by assay, organ, biosample, or target
Command definition
search-encode.mdname: search-encode description: Search ENCODE experiments by assay, organ, biosample, or target
Search the ENCODE Project for experiments matching the user's criteria.
Use the `encode_search_experiments` tool with filters like assay_title, organ, biosample_term_name, and target. Start with `encode_get_facets` if the user is exploring what data exists. Use `encode_get_metadata` to discover valid filter values.
Refer to the search-encode skill for detailed guidance.
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Repo: ammawla/encode-toolkit
Other commands on encode-toolkit.
- /browse-files
List, search, and inspect ENCODE files by format, type, and assembly
Open command - /cite-encode
Generate ENCODE citations for publications, grants, and presentations
Open command - /compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
Open command - /cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Open command - /download-encode
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
Open command - /log-provenance
Log derived files and trace provenance back to ENCODE source data
Open command