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Best practices for using the ENCODE Toolkit MCP tools and API.
MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines
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Best practices for using the ENCODE Toolkit MCP tools and API.
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ENCODE data quality standards and QC thresholds for genomics experiments.
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ENCODE file format conventions and genomics data handling best practices.
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Data provenance and reproducibility standards for ENCODE analysis workflows.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: