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Maftools-MCP

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Maftools-MCP

Maftools-MCP exposes R maftools analyses through the Model Context Protocol (MCP). An MCP-compatible client can translate a natural-language request into calls for mutation summaries, oncoplots, cohort comparisons, mutation signatures, clinical enrichment, survival analyses, and copy-number visualization.

The server includes the 59 tools counted in the manuscript, plus the export_r_script validation utility: 60 registered tools in total. See the complete tool reference for inputs, defaults, outputs and underlying R functions. R code is executed through rpy2. ANNOVAR annotation is an optional external workflow; the server's conversion tool consumes annotated multianno files, not unannotated VCFs.

Installation

The packaged Docker image is available from Docker Hub:

docker pull lin97/maftools-mcp:v.1.1.0

For an immutable image reference, use the recorded digest:

docker pull lin97/maftools-mcp@sha256:d7dc8ed2ea12c1a9ee9e60a4f304ab056a53e5cfa1d4780871603ed875ef2b86

For setup instructions, MCP client configuration, and usage examples, see the Maftools-MCP tutorial.

Related MCP server: Liana-MCP

Code Availability

The Maftools-MCP source code is publicly available in this GitHub repository:

https://github.com/linchinghsuan/maftools-mcp

The Python MCP server source is located in src/maftools_mcp/. The repository also includes the complete tool reference, machine-readable tool schema, and curated validation materials in docs/ and validation/.

The packaged environment is documented in docs/environment.md, including the Docker image digest and the observed Python, R, maftools, and ANNOVAR workflow versions. The machine-readable image record is available at environment/observed-docker-image.json.

Validation materials

The validation directory contains the detailed records supporting the Supplementary Tables. The corresponding materials are organized as follows:

Supplementary table

Validation materials

Supplementary Table S1

validation/Stage_1_mcp_inspector/ and validation/Stage_2_LLM_validation/ contain the detailed MCP Inspector and LLM validation records.

Supplementary Table S2

validation/Use-case_evaluation/repeated_run/ contains the repeated-run evaluation materials.

Supplementary Table S3

validation/ANNOVAR_skill+maftools-mcp/ contains the ANNOVAR skill and Maftools-MCP evaluation materials.

Supplementary Table S4

validation/Use-case_evaluation/prompt_robustness/ contains the prompt-robustness evaluation materials.

These directories include the relevant inputs, execution records, generated outputs, comparison files, scripts, and figures where available. The validation materials are provided for review and provenance; ANNOVAR itself and restricted third-party data or databases are not redistributed.

License

Maftools-MCP code is available under the MIT License. R, maftools, ANNOVAR and other dependencies retain their own licenses. This repository does not grant redistribution rights for third-party datasets or ANNOVAR assets.

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