How do I connect Encode Toolkit MCP Server to Claude?

The listing records `claude mcp add encode -- uvx encode-toolkit` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Claude Code, Cursor as compatible clients.

Is Encode Toolkit MCP Server free?

The listed licence is AGPL-3.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Encode Toolkit MCP Server do?

Encode Toolkit MCP Server documents 20 tools to the agent, including encode_batch_download, encode_compare_experiments, encode_download_files. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Encode Toolkit

Unclaimed

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

Install

$claude mcp add encode -- uvx encode-toolkit

Set up this server

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This server needs project-specific setup. Follow the project instructions; no reusable public launch command is available yet.

Project instructions

aiai-agentsai-biobioinformaticsbioinformatics-toolclaudeclaude-codeclaude-code-mcpclaude-code-pluginclaude-code-skills

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20 of 20 tools

Documented tools (20)

From project documentation. A server handshake does not verify each tool’s description or behavior.

encode_batch_download

Search + download in one step. Runs in preview mode by default.

encode_compare_experiments

Analyze whether two experiments are compatible for combined analysis.

encode_download_files

Download specific files by accession to a local directory.

encode_export_data

Export tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.

encode_get_citations

Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.

encode_get_experiment

Get full details for a single experiment including all files, quality metrics, and audit info.

encode_get_facets

Get live counts from ENCODE showing what data exists for given filters.

encode_get_file_info

Get detailed metadata for a single file.

encode_get_metadata

List valid filter values for any parameter.

encode_get_provenance

View provenance chains from derived files back to source ENCODE data.

encode_get_references

Get external references linked to tracked experiments for cross-server workflows.

encode_link_reference

Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.

encode_list_files

List files for a specific experiment with format/type filters.

encode_list_tracked

List all experiments in your local tracker with metadata, publication counts, and derived file counts.

encode_log_derived_file

Log a file you created from ENCODE data for provenance tracking.

encode_manage_credentials

Store, check, or clear ENCODE credentials for restricted data access.

encode_search_experiments

Search ENCODE experiments with 20+ filters.

encode_search_files

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

encode_summarize_collection

Get grouped statistics of your tracked experiment collection.

encode_track_experiment

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

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Encode Toolkit MCP Server

How do I connect Encode Toolkit MCP Server to Claude?: The listing records `claude mcp add encode -- uvx encode-toolkit` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Claude Code, Cursor as compatible clients.
Is Encode Toolkit MCP Server free?: The listed licence is AGPL-3.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Encode Toolkit MCP Server do?: Encode Toolkit MCP Server documents 20 tools to the agent, including encode_batch_download, encode_compare_experiments, encode_download_files. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.