Command
browse-files
List, search, and inspect ENCODE files by format, type, and assembly
@ammawlaView CommandData
Command
/cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Install
> /plugin marketplace add ammawla/encode-toolkit > /plugin install encode-toolkit@ammawla
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.
Ships withencode-toolkit
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Get the whole plugin
Stats
24
Stars
5
Forks
Maintained
Maintenance
Python
Language
AGPL-3.0
License
1mo ago
Last commit
6mo ago
Created
Repo: ammawla/encode-toolkit
Other commands on encode-toolkit.
@ammawlaView CommandCommand
cite-encode
Generate ENCODE citations for publications, grants, and presentations
@ammawlaView CommandCommand
compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
@ammawlaView CommandCommand
download-encode
Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@ammawlaView CommandCommand
Command
manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
@ammawlaView Command