browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/manage-credentials
Store, check, or clear ENCODE API credentials for restricted data
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
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 (needs both `access_key` and `secret_key`), "check" to verify configuration, or "clear" to remove stored credentials. Credentials go to your OS keyring (macOS Keychain, Linux Secret Service, Windows Credential Locker), falling back to a Fernet-encrypted file at `~/.encode_connector/credentials.enc` when no keyring is available.
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.
2047 skills7 agents1 MCP
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Other commands on encode-toolkit.
@ammawlaInstall Commandcite-encode
CommandGenerate ENCODE citations for publications, grants, and presentations
@ammawlaInstall Commandcompare-experiments
CommandCheck if two ENCODE experiments are compatible for combined analysis
@ammawlaInstall Commandcross-reference
CommandCross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
@ammawlaInstall Commanddownload-encode
CommandDownload ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification
@ammawlaInstall Commandlog-provenance
CommandLog derived files and trace provenance back to ENCODE source data
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