ammawla

Cross Reference — Data skill for Claude Code

Data community

Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv.

How to install Cross Reference

Installs to ~/.claude/skills/ammawla-encode-toolkit-cross-reference/SKILL.md

Terminal

mkdir -p ~/.claude/skills/ammawla-encode-toolkit-cross-reference && curl -fsSL https://raw.githubusercontent.com/ammawla/encode-toolkit/HEAD/commands/cross-reference.md -o ~/.claude/skills/ammawla-encode-toolkit-cross-reference/SKILL.md

Restart Claude Code, or start a new session, for it to be picked up.

What Cross Reference does

name: cross-reference description: Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv

Link ENCODE experiments with external databases for integrated analysis.

Use `encode_link_reference` to attach PMIDs, DOIs, GEO accessions, or NCT IDs. Use `encode_get_references` to retrieve linked identifiers. Works with PubMed, bioRxiv, ClinicalTrials.gov, and GEO MCP servers.

Refer to the cross-reference skill for detailed guidance.

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