browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/cite-encode
Generate ENCODE citations for publications, grants, and presentations
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
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.
2047 skills7 agents1 MCP
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Other commands on encode-toolkit.
@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
@ammawlaInstall Commandmanage-credentials
CommandStore, check, or clear ENCODE API credentials for restricted data
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