# ENCODE Toolkit

Twenty tools and 47 skills over the ENCODE Project: find experiments, pull data, run analysis pipelines and cross-reference other genomics databases.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 21
- Author: ammawla
- License: AGPL-3.0 · policy=link-only · description only; the file stays with the author
- Source: https://github.com/ammawla/encode-toolkit
- Updated: 2026-09-27
- HTML: https://affpapa.org/en/nevibecode/mcp/encode-toolkit

## What it does

The server connects your agent to the live ENCODE API. Ask for histone ChIP-seq in a given tissue, get the experiments, download the files, then run one of the bundled pipelines. Skills cover the neighbouring resources too: GTEx expression, ClinVar significance, GWAS Catalog associations, gnomAD frequencies, Ensembl annotation, UCSC tracks and JASPAR motifs.

Nothing to authenticate against — these are public databases. You do need Node.js, because the server starts through `npx -y encode-toolkit`.

The release is marked beta at 0.3.4. Fine for exploratory work; if results feed a paper, test your own queries on known data first. Licensing is AGPL-3.0, so shipping it inside a hosted product carries copyleft obligations.

## Requirements
- Needs: Node.js (commands run via npx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add encode-toolkit -- npx -y encode-toolkit
```

### Codex

**Platform CLI**
```bash
codex mcp add encode-toolkit -- npx -y encode-toolkit
```

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "encode-toolkit": {
            "command": "npx",
            "args": [
                "-y",
                "encode-toolkit"
            ]
        }
    }
}
```

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "encode-toolkit": {
            "type": "stdio",
            "command": "npx",
            "args": [
                "-y",
                "encode-toolkit"
            ]
        }
    }
}
```

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add encode-toolkit npx -y encode-toolkit
```

## When to use it
- locate ChIP-seq experiments by tissue and target
- download ENCODE files without sorting formats by hand
- check variant significance against ClinVar
- line up peaks with GWAS Catalog positions
- draft a methods section with source references

## Example prompts
- Find every histone ChIP-seq experiment for human pancreas tissue
- Download the peaks for that experiment and list nearby genes
- Cross-check these variants in ClinVar and gnomAD, then build a table

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NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md