Command
browse-files
List, search, and inspect ENCODE files by format, type, and assembly
@ammawlaView CommandData
Command
/cite-encode
Generate ENCODE citations for publications, grants, and presentations
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
/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.
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
compare-experiments
Check if two ENCODE experiments are compatible for combined analysis
@ammawlaView CommandCommand
cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@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