encode_manage_credentials
Store, check, or clear ENCODE credentials for restricted data access.
How to use it
encode_manage_credentials is exposed by the Encode Toolkit MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the encode_manage_credentials tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.
Install Encode Toolkit
claude mcp add encode -- uvx encode-toolkitOther tools in Encode Toolkit (39)
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Search + download in one step. Runs in preview mode by default.
Analyze whether two experiments are compatible for combined analysis.
Download specific files by accession to a local directory.
Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.
Get full details for a single experiment including all files, quality metrics, and audit info.
Get live counts from ENCODE showing what data exists for given filters.
Get detailed metadata for a single file.
List valid filter values for any parameter.
List files for a specific experiment with format/type filters.
List all experiments in your local tracker with metadata, publication counts, and derived file counts.
Search ENCODE experiments with 20+ filters.
Search files across all experiments with combined experiment + file filters.
Track an experiment locally with its publications, methods, and pipeline info.
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