ammawla/encode-toolkit

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
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Quick Start
Claude Code Plugin (recommended)
Start a new Claude Code session and enter:
That's it. All 20 tools, 47 skills, and the MCP connector are now available.
MCP-only install (tools only, no skills)
If you only need the 20 MCP tools without the 47 workflow skills:
Other editors and platforms
npx (Node.js)
Or in MCP client config: { "command": "npx", "args": ["encode-toolkit"] }
pip install
Then use encode-toolkit as the command in any MCP client configuration:
Claude Desktop (MCP only)
Add to your claude_desktop_config.json:
**macOS**: ~/Library/Application Support/Claude/claude_desktop_config.json
**Windows**: %APPDATA%\Claude\claude_desktop_config.json
> No installation needed when using uvx. Just add the config and restart Claude.
VS Code / Copilot
Add to .vscode/mcp.json in your workspace:
Cursor
Add to .cursor/mcp.json:
Windsurf
Add to .windsurf/mcp.json:
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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"*
More example prompts
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"*