ENCODE Toolkit
This connects Claude to the ENCODE Project's genomics data repository and chains together 13 additional databases including GTEx, ClinVar, GWAS Catalog, JASPAR, and gnomAD. The 20 MCP tools handle search, metadata retrieval, and file downloads from ENCODE's REST API. The 48 skills are workflow recipes that guide Claude through multi-step analysis patterns like ChIP-seq peak calling, cross-referencing variants with regulatory elements, pulling tissue expression profiles, and generating methods sections with full provenance tracking. Built for researchers who need to move from "find all H3K27ac ChIP-seq in pancreas" to downloaded BEDfiles, overlap analysis with GWAS hits, motif scanning, and a citable audit trail without leaving the conversation. Ships as a Claude Code plugin or standalone MCP server with 98% test coverage and no telemetry.
- GitHub stars
- 35
- tools
- 20
- transport
- STDIO
- last updated
- Mar 9, 2026
Tools
20 toolsPublic tool metadata for what this MCP can expose to an agent.
encode_search_experimentsSearch ENCODE experiments with 20+ filters.
Search ENCODE experiments with 20+ filters.
No parameter schema in public metadata yet.
encode_get_experimentGet full details for a single experiment including all files, quality metrics, and audit info.
Get full details for a single experiment including all files, quality metrics, and audit info.
No parameter schema in public metadata yet.
encode_download_filesDownload specific files by accession to a local directory.
Download specific files by accession to a local directory.
No parameter schema in public metadata yet.
encode_batch_downloadSearch + download in one step. Runs in preview mode by default.
Search + download in one step. Runs in preview mode by default.
No parameter schema in public metadata yet.
encode_track_experimentTrack an experiment locally with its publications, methods, and pipeline info.
Track an experiment locally with its publications, methods, and pipeline info.
No parameter schema in public metadata yet.
encode_list_filesList files for a specific experiment with format/type filters.
List files for a specific experiment with format/type filters.
No parameter schema in public metadata yet.
encode_search_filesSearch files across all experiments with combined experiment + file filters.
Search files across all experiments with combined experiment + file filters.
No parameter schema in public metadata yet.
encode_get_metadataList valid filter values for any parameter.
List valid filter values for any parameter.
No parameter schema in public metadata yet.
encode_get_facetsGet live counts from ENCODE showing what data exists for given filters.
Get live counts from ENCODE showing what data exists for given filters.
No parameter schema in public metadata yet.
encode_get_file_infoGet detailed metadata for a single file.
Get detailed metadata for a single file.
No parameter schema in public metadata yet.
encode_manage_credentialsStore, check, or clear ENCODE credentials for restricted data access.
Store, check, or clear ENCODE credentials for restricted data access.
No parameter schema in public metadata yet.
encode_list_trackedList all experiments in your local tracker with metadata, publication counts, and derived file counts.
List all experiments in your local tracker with metadata, publication counts, and derived file counts.
No parameter schema in public metadata yet.
encode_get_citationsGet publications for tracked experiments. Export as BibTeX or RIS for reference managers.
Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.
No parameter schema in public metadata yet.
encode_compare_experimentsAnalyze whether two experiments are compatible for combined analysis.
Analyze whether two experiments are compatible for combined analysis.
No parameter schema in public metadata yet.
encode_summarize_collectionGet grouped statistics of your tracked experiment collection.
Get grouped statistics of your tracked experiment collection.
No parameter schema in public metadata yet.
encode_log_derived_fileLog a file you created from ENCODE data for provenance tracking.
Log a file you created from ENCODE data for provenance tracking.
No parameter schema in public metadata yet.
encode_get_provenanceView provenance chains from derived files back to source ENCODE data.
View provenance chains from derived files back to source ENCODE data.
No parameter schema in public metadata yet.
encode_export_dataExport tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.
Export tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.
No parameter schema in public metadata yet.
encode_link_referenceLink external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.
Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.
No parameter schema in public metadata yet.
encode_get_referencesGet external references linked to tracked experiments for cross-server workflows.
Get external references linked to tracked experiments for cross-server workflows.
No parameter schema in public metadata yet.
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Details
- Repository
- github.com/ammawla/encode-toolkit
- Category
- Search & Web Crawling
- Package
encode-toolkit- Transport
- STDIO
- Registry
- MCP registry, active
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