encode_get_references

MCP tool from Encode Toolkit by ammawla

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

How to use it

Project documentation lists encode_get_references for the Encode Toolkit MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install Encode Toolkit

$claude mcp add encode -- uvx encode-toolkit
FULL ENCODE TOOLKIT LISTING

Other tools in Encode Toolkit (19)

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_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.