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ENCODE Toolkit MCP

An open-source MCP server and Claude Code plugin that provides 20 tools and 47 skills for accessing and analyzing ENCODE Project genomic data. It enables users to search and download ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, and CUT&RUN data, cross-reference 14 databases, run 7 Nextflow pipelines, and generate publication-ready methods with full provenance directly from natural language prompts.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

ENCODE Toolkit MCP logo, by Alex M. MawlaCommunity listingLocal stdioSource reviewed; not executedPublished by Alex M. Mawla
Vendor documentation

What you can do with it

  • Search and download ENCODE genomic datasets
  • Analyze ChIP-seq, ATAC-seq, and RNA-seq data
  • Cross-reference data with 14 external databases
  • Run 7 Nextflow analysis pipelines

Source and maintenance

Community listingRegistry 0.3.0-beta.5
mcp-registry: io.github.ammawla/encode-toolkit@0.3.0-beta.5Source repository
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

encode-toolkit 0.3.0-beta.5

npm
encode-toolkit package definition
{
  "version": "0.3.0-beta.5",
  "transport": "stdio",
  "identifier": "encode-toolkit",
  "registryType": "npm"
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "encode-toolkit-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "encode-toolkit-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "encode-toolkit-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "encode-toolkit-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

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