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ENCODE Toolkit

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

MCP server · by ammawla

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About

ENCODE Toolkit is an MCP server published by ammawla. Marketplaces we read that list it: 2 (Official MCP Registry, Community GitHub marketplaces). We first saw it on 2026-10-11 and have recorded no change since. As of our marketplace pass on 2026-10-14.

What it asks for

  • Runs on your machine

None of the marketplaces we read publishes its tools or the settings it asks for.

What it declares, asks for and runs, in full

Only install plugins from developers you trust. We list what marketplaces publish and do not test plugins.

Package

npm encode-toolkit (encode-toolkit on npm)

  • npm downloads/week: 67 (2026-10-13)
  • npm downloads/month: 838 (2026-10-13)
  • Latest version on npm: 0.3.4, published 2026-09-21
  • Declared version 0.3.0-beta.5 is not listed on npm

npm facts come from the public npm registry (registry.npmjs.org, api.npmjs.org). Each figure is the registry's own and is never added to another. A registry that publishes no figure shows none: no number is not zero.

Works with

  • Claude Code
  • Codex
  • Cursor
  • VS Code
  • Copilot CLI
Install in CursorInstall in VS Code

A one-click link opens the client, which asks you to confirm before it adds the server.

From the marketplaces that list it and the MCP transport it declares, as each client documents them. We do not test plugins.

Connect

Commands and configs built only from what its marketplaces declare. We do not run them for you and do not test plugins.

As a local MCP server: npm package

Built from what Official MCP Registry declares.

Claude CodeTerminal
claude mcp add --transport stdio encode-toolkit -- npx -y encode-toolkit
Codex~/.codex/config.toml
[mcp_servers.encode-toolkit]
command = "npx"
args = ["-y", "encode-toolkit"]
Cursor~/.cursor/mcp.json
{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

As a Claude Code plugin

Built from what Community GitHub marketplaces declares.

Claude CodeInside a Claude Code session
/plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkit@ammawla

Where it is published

MarketplaceStatusVersionFiguresVerifiedFirst seen
Official MCP Registry (Open the registry record) Listed 0.3.0-beta.5 Downloads/month (npm): 838
Downloads/week (npm): 67
Forks (GitHub): 5
Stars (GitHub): 21		 Not marked

Each figure is the marketplace's own and is never added up across marketplaces. A marketplace that publishes no figure shows none: no number is not zero.

Also listed in one community marketplace
MarketplaceRepositoryStars (GitHub)
ammawla ammawla/encode-toolkit 21

Which marketplaces we read and how we check them

What the bundle contains

As published on Community GitHub marketplaces.

MCP servers: 1

  • encode-toolkit

Skills: 47

  • accessibility-aggregation
  • batch-analysis
  • bioinformatics-installer
  • cellxgene-context
  • cite-encode
  • clinvar-annotation
  • compare-biosamples
  • cross-reference
  • data-provenance
  • disease-research
  • download-encode
  • ensembl-annotation
Show the remaining 35
  • epigenome-profiling
  • functional-screen-analysis
  • geo-connector
  • gnomad-variants
  • gtex-expression
  • gwas-catalog
  • hic-aggregation
  • histone-aggregation
  • integrative-analysis
  • jaspar-motifs
  • liftover-coordinates
  • methylation-aggregation
  • motif-analysis
  • multi-omics-integration
  • peak-annotation
  • pipeline-atacseq
  • pipeline-chipseq
  • pipeline-cutandrun
  • pipeline-dnaseseq
  • pipeline-guide
  • pipeline-hic
  • pipeline-rnaseq
  • pipeline-wgbs
  • publication-trust
  • quality-assessment
  • regulatory-elements
  • scientific-writing
  • scrna-meta-analysis
  • search-encode
  • setup
  • single-cell-encode
  • track-experiments
  • ucsc-browser
  • variant-annotation
  • visualization-workflow

Commands: 10

  • browse-files
  • cite-encode
  • compare-experiments
  • cross-reference
  • download-encode
  • log-provenance
  • manage-credentials
  • quality-check
  • search-encode
  • track-experiments

Agents: 7

  • atacseq-pipeline
  • chipseq-pipeline
  • cutandrun-pipeline
  • dnaseseq-pipeline
  • hic-pipeline
  • rnaseq-pipeline
  • wgbs-pipeline

What changed

  1. Appeared on a new marketplace: Community GitHub marketplaces
  2. Community GitHub marketplaces: appeared

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Found by meaning, not by shared code or a shared repository: similar plugins stay separate products, and this is not a review or a recommendation.

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Data comes from the Official MCP Registry (registry.modelcontextprotocol.io), CC0 1.0. Data comes from public marketplace files in GitHub repositories of their authors. Figures come from our own regular passes over the marketplaces, last read on . We publish no contact details for plugin publishers.

Where the data comes from: how the catalog is built