Add plugin microbe

plugins/Presisitence/microbe/LICENSE

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+MIT License
+
+Copyright (c) 2026 Presisitence
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

plugins/Presisitence/microbe/README.md

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+# microbe
+
+Downstream **16S / ITS** microbiome analysis for MiniMax Code. vegan, DESeq2, edgeR, igraph,
+Hmisc, randomForest, and ggtree scripts are wrapped as MCP tools and rendered by local **Rscript**.
+
+Figure types follow two public papers for layout (the Plugin does not include their data):
+
+- Liu et al. 2023, *Nature Microbiology*
+- Zhou et al. 2022, *Nature Communications*
+
+Does not run DADA2/QIIME2. Start from a feature table.
+
+## Try it
+
+```text
+I have feature_table.csv, taxonomy.csv, and metadata.csv (groups DP vs DSP). Draw alpha and beta
+diversity, a genus stacked bar, DESeq2 differential abundance, and a co-occurrence network.
+```
+
+Expected result: the agent calls `microbe_env`, then `microbe_alpha`, `microbe_beta`,
+`microbe_composition`, `microbe_diff`, and `microbe_network`. png+pdf paths and key statistics
+are returned. Synthetic tables can be generated with `python tests/prep_test.py` for a dry run.
+
+## Requirements
+
+- Python 3.10+ and [uv](https://docs.astral.sh/uv/) on PATH.
+- R with `Rscript` on PATH, or set `MICROBE_RSCRIPT`.
+- R packages such as vegan, ggplot2, igraph; DESeq2/edgeR optional (tools degrade with install hints).
+- Windows, macOS, and Linux.
+
+## Data and network
+
+- Analyses are local on user CSVs. No telemetry.
+- No credentials in the package.
+- `tests/prep_test.py` writes synthetic OTU-like tables only.
+
+## License
+
+MIT. See [LICENSE](LICENSE).

plugins/Presisitence/microbe/mcp.json

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+{
+  "$schema": "https://agent-plugins.org/schemas/1.0.0/mcp.schema.json",
+  "mcpServers": {
+    "microbe": {
+      "type": "stdio",
+      "command": "uv",
+      "args": ["run", "server.py"],
+      "cwd": "${PLUGIN_ROOT}"
+    }
+  }
+}

plugins/Presisitence/microbe/microbe_toolkit/__init__.py

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+"""microbe_toolkit: 把一套下游微生物组/扩增子分析 R 脚本参数化封装为 MCP 工具。"""
+from __future__ import annotations
+
+from . import runner
+
+__all__ = ["runner"]

plugins/Presisitence/microbe/microbe_toolkit/cli.py

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+"""命令行自检入口：`microbe-cli` 检查 R 引擎与关键微生物组分析包是否就绪。"""
+from __future__ import annotations
+
+import sys
+
+from . import runner
+
+_KEY_PKGS = [
+    "vegan", "ggplot2", "ggpubr", "dplyr", "tidyr", "reshape2", "pheatmap",
+    "ggrepel", "igraph", "Hmisc", "randomForest", "ape", "scales", "circlize",
+    "ggalluvial", "edgeR", "DESeq2", "ggtree", "phyloseq", "SpiecEasi",
+]
+
+
+def main() -> int:
+    rscript = runner.find_rscript()
+    print(f"Rscript: {rscript or '未找到 (设置 MICROBE_RSCRIPT 或安装 R)'}")
+    print(f"mscripts 目录: {runner.mscripts_dir()}")
+    if not rscript:
+        return 1
+    status = runner.check_packages(_KEY_PKGS, rscript=rscript)
+    print("\nR 包状态:")
+    for pkg, ok in status.items():
+        print(f"  [{'x' if ok else ' '}] {pkg}")
+    missing = [p for p, ok in status.items() if not ok]
+    if missing:
+        print("\n缺失包安装建议:")
+        print("  " + runner._install_hint(missing))
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())