About Fganalysis MCP Server
Fganalysis MCP Server is an MCP server in the Agents category: an MCP server that exposes the fganalysis R package to agentic workflows. The server is designed for tools such as ClawBio that need structured access to FinnGen lab, drug-purchase, drug-response, BLUP-slope, median pre-drug phenotype, and ATC-code-mapping workflows.
Install
git clone https://github.com/RezaJF/fganalysis_MCP_serverThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (19)
calculate_fixed_slopesOLS per-individual slopes (BLUP-comparable baseline).
Parameters not published.
clear_atc_mappings_cacheClears the in-memory ATC mapping cache.
Parameters not published.
compute_drug_purchase_cadencePer-VNR purchase-interval (cadence) statistics.
Parameters not published.
execute_r_codeExecutes focused R snippets with `conn` and exported `fganalysis` functions in scope.
Parameters not published.
generate_analysis_notebookOptional notebook generation, requiring `google-generativeai`.
Parameters not published.
get_atc_code_relationshipsExpands ATC codes and returns historical/current relationships.
Parameters not published.
get_drug_purchasesCounts and previews purchases for ATC code prefixes, with optional ATC mapping.
Parameters not published.
get_first_drug_purchaseReturns the first qualifying drug purchase per FINNGENID.
Parameters not published.
get_lab_data_summaryCounts and previews selected OMOP lab concept IDs.
Parameters not published.
get_measurements_before_drugExtracts pre-drug lab measurements (with exposed/unexposed indicators).
Parameters not published.
Show all 19 tools
get_median_pre_drug_valuesCreates GWAS-ready median pre-drug phenotype files.
Parameters not published.
inspect_fganalysis_environmentReports R, `fganalysis`, exported-function, wrapper, and optional config status.
Parameters not published.
load_atc_mappings_infoReports the active ATC mapping file metadata and preview.
Parameters not published.
plot_lab_distributionWrites before/after lab-value distribution plots.
Parameters not published.
plot_median_pre_drug_diagnosticsDiagnostic before/after MAD outlier removal plots.
Parameters not published.
process_variance_filesInverse-rank-normalises BLUP variance files and summarises results.
Parameters not published.
run_blup_analysisCalculates BLUP slopes from pre-drug longitudinal lab measurements.
Parameters not published.
run_drug_response_analysisBuilds drug-response data and writes summary plots/tables.
Parameters not published.
validate_fganalysis_configValidates the JSON connection config required by `connect_fgdata()`.
Parameters not published.
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