browse-files
CommandList, search, and inspect ENCODE files by format, type, and assembly
@ammawlaInstall CommandData
Command
/cross-reference
Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
> /plugin marketplace add ammawla/encode-toolkit> /plugin install encode-toolkit@ammawla
Command definition
cross-reference.mdname: cross-reference description: Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv
Link ENCODE experiments with external databases for integrated analysis.
The experiment must be tracked first with `encode_track_experiment`. Use `encode_link_reference` with a `reference_type` of "pmid", "doi", "nct_id", "preprint_doi", "geo_accession", or "other". Use `encode_get_references` to retrieve linked identifiers, optionally filtered by experiment or type. Tracking an experiment also auto-links the GEO and PMID entries in its ENCODE dbxrefs. Pass the retrieved identifiers to the PubMed, bioRxiv and ClinicalTrials.gov MCP servers; GEO is reached through the geo-connector skill.
Refer to the cross-reference 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
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@ammawlaInstall Commandmanage-credentials
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