/cite-encode
Generate ENCODE citations for publications, grants, and presentations
$ 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
/cite-encode
Context preview
What this command does when you run it.
Generate ENCODE citations for publications, grants, and presentations
Command definition
cite-encode.mdname: cite-encode description: Generate ENCODE citations for publications, grants, and presentations
Generate proper citations for ENCODE data and experiments.
Use `encode_get_citations` to retrieve publications in BibTeX or RIS format. Use `encode_track_experiment` first to populate citation data. Link external references with `encode_link_reference`.
Refer to the cite-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 - /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 - /manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
Open command