browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/track-experiments
Track ENCODE experiments locally with publications and provenance
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
track-experiments.mdname: track-experiments description: Track ENCODE experiments locally with publications and provenance
Track ENCODE experiments in a local SQLite database with associated publications, pipeline info, and provenance chains.
Use `encode_track_experiment` to add experiments. Use `encode_list_tracked` to view your library. Use `encode_get_citations` to export citations as BibTeX or RIS.
Refer to the track-experiments 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.
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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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