/cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
$ 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
/cross-reference
Context preview
What this command does when you run it.
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Command definition
cross-reference.mdname: cross-reference description: Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Link ENCODE experiments with external databases for integrated analysis.
Use `encode_link_reference` to attach PMIDs, DOIs, GEO accessions, or NCT IDs. Use `encode_get_references` to retrieve linked identifiers. Works with PubMed, bioRxiv, ClinicalTrials.gov, and GEO MCP servers.
Refer to the cross-reference 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 - /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 - /manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
Open command