browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/log-provenance
Log derived files and trace provenance back to ENCODE source data
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
log-provenance.mdname: log-provenance description: Log derived files and trace provenance back to ENCODE source data
Track provenance of files you create from ENCODE data.
Use `encode_log_derived_file` after creating derived files (filtered peaks, merged signals, differential analysis). Provide source accessions, tool used, and parameters. Use `encode_get_provenance` to trace any derived file back to its original ENCODE source.
Refer to the data-provenance skill for full provenance workflow 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.
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CommandGenerate ENCODE citations for publications, grants, and presentations
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@ammawlaInstall Commanddownload-encode
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@ammawlaInstall Commandmanage-credentials
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