Is Encode Toolkit safe to use?

Encode Toolkit has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under AGPL-3.0.

How do I install Encode Toolkit?

Encode Toolkit can be installed by cloning its GitHub repository and following the setup instructions in the README.

What AI clients work with Encode Toolkit?

Encode Toolkit is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.

Is Encode Toolkit actively maintained?

Encode Toolkit is actively maintained — last commit was 11 days ago. It has 34 GitHub stars.

Encode Toolkit

Name: Encode Toolkit
Author: ammawla

by ammawla

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

34 0 tools GitHub

No known CVEs

AGPL-3.0 license

Actively maintained

Last commit 11d ago

Works with most clients

Transport: stdio

0 tools

Grade F

Edit this pageView history

Health AI / ML

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

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Add this badge to your README to show your security score and help users find safe servers.

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[![MCPpedia Score](https://mcppedia.org/api/badge/encode-toolkit)](https://mcppedia.org/s/encode-toolkit)

Read me

What Encode Toolkit does

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

29/100across 5 weighted dimensions

How we score →

0255075100

−71

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Help improve this page

This server is missing a description. Tools and install config are also missing.If you've used it, help the community.

Add information

Community

Reviews

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Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Encode Toolkit safe to use?: Encode Toolkit has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under AGPL-3.0.
How do I install Encode Toolkit?: Encode Toolkit can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with Encode Toolkit?: Encode Toolkit is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.
Is Encode Toolkit actively maintained?: Encode Toolkit is actively maintained — last commit was 11 days ago. It has 34 GitHub stars.

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Community

Discussion

Start a conversation

Ask a question, share a tip, or report an issue.

Has anyone used this with Cursor?How do you handle auth?Any alternatives?

Edit this pageView history

Health AI / ML

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/encode-toolkit)](https://mcppedia.org/s/encode-toolkit)

Read me

What Encode Toolkit does

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

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.

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}
}

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.

MCP-only install (tools only, no skills)

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

claude mcp add encode -- uvx encode-toolkit

Other editors and platforms
... View full README on GitHub

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

29/100across 5 weighted dimensions

How we score →

0255075100

−71

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Help improve this page

This server is missing a description. Tools and install config are also missing.If you've used it, help the community.

Add information

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Encode Toolkit safe to use?: Encode Toolkit has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under AGPL-3.0.
How do I install Encode Toolkit?: Encode Toolkit can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with Encode Toolkit?: Encode Toolkit is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.
Is Encode Toolkit actively maintained?: Encode Toolkit is actively maintained — last commit was 11 days ago. It has 34 GitHub stars.