Command
browse-files
List, search, and inspect ENCODE files by format, type, and assembly
@ammawlaView CommandData
Command
/manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
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
/manage-credentials
Context preview
What this command does when you run it.
Store, check, or clear ENCODE API credentials for restricted data
Command definition
manage-credentials.mdname: manage-credentials description: Store, check, or clear ENCODE API credentials for restricted data
Manage ENCODE API credentials for accessing unreleased or restricted datasets.
Use `encode_manage_credentials` with action "store" to save credentials, "check" to verify configuration, or "clear" to remove stored credentials. Credentials are stored in your OS keyring (macOS Keychain, Linux Secret Service).
Most ENCODE data is public and requires no authentication.
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
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