ENCODE Toolkit MCP server

ENCODE Toolkit — Genomics Research Infrastructure for Claude

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.

Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.

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Citation Notes

If you use ENCODE-Toolkit, please cite:

Alex M. Mawla. (2026). ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis. Zenodo. https://doi.org/10.5281/zenodo.18917511

BibTeX

@software{mawla_2026_encode_toolkit,
  author  = {Mawla, Alex M.},
  title   = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis},
  year    = {2026},
  publisher = {Zenodo},
  doi     = {10.5281/zenodo.18917511},
  url     = {https://doi.org/10.5281/zenodo.18917511}
}

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Quick Start

Claude Code Plugin (recommended)

Start a new Claude Code session and enter:

/plugin marketplace add ammawla/encode-toolkit

/plugin install encode-toolkit

That's it. All 20 tools, 47 skills, and the MCP connector are now available.

If you only need the 20 MCP tools without the 47 workflow skills:

claude mcp add encode -- uvx encode-toolkit

npx (Node.js)

npx encode-toolkit

Or in MCP client config: { "command": "npx", "args": ["encode-toolkit"] }

pip install

pip install encode-toolkit

Then use encode-toolkit as the command in any MCP client configuration:

{
  "mcpServers": {
    "encode": {
      "command": "encode-toolkit"
    }
  }
}

Add to your claude_desktop_config.json:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

No installation needed when using uvx. Just add the config and restart Claude.

Add to .vscode/mcp.json in your workspace:

{
  "mcp": {
    "servers": {
      "encode": {
        "command": "uvx",
        "args": ["encode-toolkit"]
      }
    }
  }
}

Add to .cursor/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Add to .windsurf/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

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Connected Databases

ENCODE Toolkit integrates 14 databases through live API tools and guided skills.

Database	Access Method	Use Case
ENCODE	20 MCP tools (live API)	ChIP-seq, ATAC-seq, RNA-seq, Hi-C, WGBS, CUT&RUN data
GTEx	REST API (skill)	Tissue-specific gene expression across 54 tissues
ClinVar	E-utilities (skill)	Variant clinical significance and pathogenicity
GWAS Catalog	REST API (skill)	Trait-variant associations from genome-wide studies
JASPAR	REST API (skill)	Transcription factor binding motif profiles
CellxGene	Census API (skill)	Single-cell expression atlas across tissues
gnomAD	GraphQL (skill)	Population allele frequencies and gene constraint
Ensembl	REST API (skill)	VEP annotation, Regulatory Build, coordinate liftover
UCSC Genome Browser	REST API (skill)	cCRE tracks, TF clusters, sequence retrieval
GEO	E-utilities (skill)	Complementary expression/epigenomic datasets
PubMed	MCP server	Literature search and citation
bioRxiv	MCP server	Preprint discovery
ClinicalTrials.gov	MCP server	Clinical trial cross-reference
Open Targets	MCP server	Drug target identification

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What You Can Ask Claude

Search and explore

• "Find all histone ChIP-seq experiments for human pancreas tissue"
• "What ATAC-seq data is available for mouse brain?"
• "Search for RNA-seq on GM12878 cell line"
• "What histone marks have ChIP-seq data for pancreas?"

Download and track

• "Download all BED files from ENCSR133RZO to ~/data/encode"
• "Track experiment ENCSR133RZO with its publications"
• "Export citations for my tracked experiments as BibTeX"

Cross-reference databases

• "What GWAS variants overlap islet enhancers?"
• "Check ClinVar pathogenicity for rs7903146"
• "Pull GTEx expression for TCF7L2 across tissues"
• "Find JASPAR motifs for HNF4A binding sites"

Run pipelines

• "Set up a ChIP-seq pipeline for my H3K27ac experiments"
• "Run ATAC-seq analysis with ENCODE-standard QC thresholds"

Generate methods and provenance

• "Log that I created filtered_peaks.bed from ENCSR133RZO using bedtools"
• "Generate a methods section for my analysis with citations"

Experiment details

• "Show me the full details for experiment ENCSR133RZO"
• "What files are available for ENCSR133RZO?"
• "List only the BED files from ENCSR133RZO"

Bulk downloads

• "Download all FASTQs from human pancreas ChIP-seq to /data/fastqs"
• "Get the IDR thresholded peaks from these experiments"
• "Download the bigWig signal tracks for H3K27me3 in GRCh38"

Compatibility analysis

• "Are experiments ENCSR133RZO and ENCSR000AKS compatible for combined analysis?"
• "Compare these two ChIP-seq experiments"

Provenance chains

• "Show me the provenance chain for my derived files"
• "What files have I derived from ENCSR133RZO?"

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The Problem

Using genomics databases today means:

1. Navigate web portals, click through dozens of filters
2. Manually find the right experiments and files across multiple databases
3. Write custom scripts to batch download
4. Lose track of which files came from where

With ENCODE Toolkit, just tell Claude what you need:

"Find all histone ChIP-seq data for human pancreas tissue"

Claude searches ENCODE, returns a structured table of 66 experiments with targets, replicates, and file counts. Downloads are organized by experiment with MD5 verification and full provenance tracking.

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Available Tools (20)

Five core tools are shown below. The remaining 15 are collapsed for readability.

encode_search_experiments

Search ENCODE experiments with 20+ filters.

Parameter	Type	Description
assay_title	string	Assay type: "Histone ChIP-seq", "ATAC-seq", "total RNA-seq", "Hi-C", etc.
organism	string	Species (default: "Homo sapiens")
organ	string	Organ: "pancreas", "brain", "liver", "heart", "kidney", etc.
biosample_type	string	"tissue", "cell line", "primary cell", "organoid"
target	string	ChIP target: "H3K27me3", "H3K4me3", "CTCF", etc.
biosample_term_name	string	Specific biosample: "GM12878", "HepG2", etc.
limit	int	Max results (default: 25)

encode_get_experiment

Get full details for a single experiment including all files, quality metrics, and audit info.

Parameter	Type	Description
accession	string	Experiment ID (e.g., "ENCSR133RZO")

encode_download_files

Download specific files by accession to a local directory.

Parameter	Type	Description
file_accessions	list[str]	File IDs to download (e.g., ["ENCFF635JIA"])
download_dir	string	Local path to save files
organize_by	string	"flat", "experiment", "format", "experiment_format"
verify_md5	bool	Verify file integrity (default: true)

encode_batch_download

Search + download in one step. Runs in preview mode by default.

Parameter	Type	Description
download_dir	string	Local path to save files
file_format	string	File format to download
assay_title	string	Assay type filter
organ	string	Organ filter
dry_run	bool	Preview only (default: true). Set false to download.

encode_track_experiment

Track an experiment locally with its publications, methods, and pipeline info.

Parameter	Type	Description
accession	string	Experiment ID to track
fetch_publications	bool	Fetch associated publications (default: true)
fetch_pipelines	bool	Fetch pipeline/analysis info (default: true)
notes	string	Optional notes to attach

encode_list_files

List files for a specific experiment with format/type filters.

Parameter	Type	Description
experiment_accession	string	Experiment ID
file_format	string	"fastq", "bam", "bed", "bigWig", "bigBed", etc.
output_type	string	"reads", "peaks", "signal", "alignments", etc.
assembly	string	"GRCh38", "mm10", etc.
preferred_default	bool	Only return recommended files

encode_search_files

Search files across all experiments with combined experiment + file filters.

Parameter	Type	Description
file_format	string	File format filter
assay_title	string	Assay type of parent experiment
organ	string	Organ of parent experiment
target	string	ChIP/CUT&RUN target
output_type	string	Output type filter
assembly	string	Genome assembly

encode_get_metadata

List valid filter values for any parameter.

Parameter	Type	Description
metadata_type	string	"assays", "organisms", "organs", "biosample_types", "file_formats", "output_types", "assemblies"

encode_get_facets

Get live counts from ENCODE showing what data exists for given filters.

Parameter	Type	Description
assay_title	string	Pre-filter by assay
organism	string	Pre-filter by organism
organ	string	Pre-filter by organ

encode_get_file_info

Get detailed metadata for a single file.

Parameter	Type	Description
accession	string	File ID (e.g., "ENCFF635JIA")

encode_manage_credentials

Store, check, or clear ENCODE credentials for restricted data access.

Parameter	Type	Description
action	string	"store", "check", or "clear"
access_key	string	ENCODE access key (for "store")
secret_key	string	ENCODE secret key (for "store")

encode_list_tracked

List all experiments in your local tracker with metadata, publication counts, and derived file counts.

Parameter	Type	Description
assay_title	string	Filter by assay type
organism	string	Filter by organism
organ	string	Filter by organ

encode_get_citations

Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.

Parameter	Type	Description
accession	string	Specific experiment (or all if omitted)
export_format	string	"json" (default), "bibtex", or "ris"

encode_compare_experiments

Analyze whether two experiments are compatible for combined analysis.

Parameter	Type	Description
accession1	string	First experiment ID
accession2	string	Second experiment ID

encode_summarize_collection

Get grouped statistics of your tracked experiment collection.

Parameter	Type	Description
assay_title	string	Filter by assay type
organism	string	Filter by organism
organ	string	Filter by organ

encode_log_derived_file

Log a file you created from ENCODE data for provenance tracking.

Parameter	Type	Description
file_path	string	Path to your derived file
source_accessions	list[str]	ENCODE accessions this was derived from
description	string	What the file contains
tool_used	string	Tool/software used
parameters	string	Command or parameters used

encode_get_provenance

View provenance chains from derived files back to source ENCODE data.

Parameter	Type	Description
file_path	string	Get provenance for a specific file
source_accession	string	List all files derived from an accession

encode_export_data

Export tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.

Parameter	Type	Description
format	string	"csv" (default), "tsv", or "json"
assay_title	string	Filter by assay type

encode_link_reference

Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.

Parameter	Type	Description
experiment_accession	string	ENCODE experiment accession
reference_type	string	"pmid", "doi", "nct_id", "preprint_doi", "geo_accession", "other"
reference_id	string	The identifier value

encode_get_references

Get external references linked to tracked experiments for cross-server workflows.

Parameter	Type	Description
experiment_accession	string	Filter by experiment (optional)
reference_type	string	Filter by type (optional)

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Authentication

Most ENCODE data is public and requires no authentication. Just install and use.

For restricted/unreleased data, ask Claude: "Store my ENCODE credentials"

Credentials are encrypted using your OS keyring (macOS Keychain, Linux Secret Service, Windows Credential Locker) and never stored in plaintext. Get your access keys from your ENCODE profile.

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Plugin Skills (47)

When installed as a Claude Code plugin, ENCODE Toolkit includes 47 literature-backed workflow skills that guide Claude through complex genomics tasks. Each analysis skill includes evidence-based quality thresholds, assay-specific metrics, and citations to primary literature.