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ENCODE Toolkit MCP server

by ammawla·io.github.ammawla/encode-toolkit·v0.3.0-beta.5·21 stars
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20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

A92/100grade A
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Safety scan
A92/100

full report

Adoption
Growing

21 stars614 downloads/wk

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If you have run it, two minutes of your experience saves the next person an afternoon.

ENCODE Toolkit tools (20)

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Read from the package source without running it. The installed server may list more.

  • encode_batch_download

    Search for files and download them all in batch.

  • encode_compare_experiments

    Analyze whether two ENCODE experiments are compatible for combined analysis.

  • encode_download_files

    Download specific ENCODE files by accession to a local directory.

  • encode_export_data

    Export tracked experiments as a table (CSV, TSV, or JSON).

  • encode_get_citations

    Get publications and citations for tracked experiments.

  • encode_get_experiment

    Get full details for a specific ENCODE experiment by accession ID.

  • encode_get_facets

    Get live filter counts from ENCODE to discover what data is available.

  • encode_get_file_info

    Get detailed information about a specific ENCODE file.

  • encode_get_metadata

    Get available filter values for ENCODE searches.

  • encode_get_provenance

    Get provenance information for derived files.

  • encode_get_references

    Get external references linked to tracked experiments.

  • encode_link_reference

    Link an external reference to a tracked ENCODE experiment.

  • encode_list_files

    List all files for a specific ENCODE experiment, with optional filters.

  • encode_list_tracked

    List all experiments you've tracked locally, with optional filters.

  • encode_log_derived_file

    Log a file you've derived from ENCODE data for provenance tracking.

  • encode_manage_credentials

    Manage ENCODE API credentials for accessing restricted/unreleased data.

  • encode_search_experiments
  • encode_search_files

    Search files across ALL experiments with combined experiment + file filters.

  • encode_summarize_collection

    Summarize your tracked experiment collection with grouped statistics.

  • encode_track_experiment

    Track an ENCODE experiment locally with its publications, methods, and pipeline info.

Public scan report

scanner v0.1.10 · 2026-09-28 · same rubric, same numbers if you re-run it

no findings
  • Code scan2 source files scanned; 32 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 1 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10
Overall 92/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

Install ENCODE Toolkit in Claude Code, Cursor or VS Code

Runs npx -y encode-toolkit on your machine. Read the scan report first; the gateway never runs local packages.

claude mcp add encode-toolkit -- npx -y encode-toolkit
Add to Cursor

What the publisher says

From the ENCODE Toolkit repository's README, as published. We do not edit it. Read it on GitHub

ENCODE Toolkit — Genomics Research Infrastructure for Claude

<!-- mcp-name: io.github.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.

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

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

ENCODE Toolkit: common questions

Is ENCODE Toolkit MCP server safe?
Yes, by our scan: it is graded A (92/100). Read the ENCODE Toolkit safety report
How do I install ENCODE Toolkit?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does ENCODE Toolkit need an API key?
Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is ENCODE Toolkit maintained?
The last commit was 16 days ago (2026-09-27). The latest release is v0.3.0-beta.5.
What can I use instead of ENCODE Toolkit?
Servers from other publishers that do the same job: HeyClaude — Claude & AI workflow directory MCP server, Arxiv MCP server and HIG Doctor MCP server. Compare all ENCODE Toolkit alternatives.

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