MCP Servers

microbe-mcp

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

Category

README

microbe-mcp

下游 微生物组 / 扩增子（16S · ITS） 分析 MCP。把 vegan / DESeq2 / edgeR / igraph / Hmisc / randomForest / ggtree 等 R 脚本封装为工具，由本机 Rscript 产出 png + pdf。

图型对齐两篇公开论文（便于复刻布局，不附带其原始数据）：

Liu et al. 2023, Nature Microbiology — 稻曲病叶际菌群
Zhou et al. 2022, Nature Communications — 番茄枯萎病跨界合成菌群

R 引擎

优先级：MICROBE_RSCRIPT → PATH 上的 Rscript → C:\Program Files\R\... / 注册表。

$env:MICROBE_RSCRIPT = "C:\Program Files\R\R-4.5.1\bin\Rscript.exe"
uv run microbe-cli

数据契约（3 张 CSV）

文件	必需列
`feature_table.csv`	`feature_id` + 各样本计数
`taxonomy.csv`	`feature_id` + 界门纲目科属种，或 QIIME 分号串
`metadata.csv`	`sample_name` + `group`；可选环境/代谢物数值列

工具（9）

microbe_env microbe_alpha microbe_beta microbe_composition microbe_diff microbe_network microbe_rf microbe_corr microbe_tree

不含 reads → ASV（DADA2/QIIME2）。已有特征表即可接入。

测试

python tests/prep_test.py   # 合成扩增子表，无真实样本
python tests/smoke.py

注册

{
  "mcpServers": {
    "microbe": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/microbe-mcp", "server.py"],
      "env": { "MICROBE_RSCRIPT": "/path/to/Rscript" }
    }
  }
}

许可

MIT。

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