Add plugin rnaseq-plot

plugins/Presisitence/rnaseq-plot/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/rnaseq-plot/README.md

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+# rnaseq-plot
+
+RNA-seq **downstream plotting** for MiniMax Code (formerly published as `rgraph`).
+Parameterized R scripts (ggplot2, pheatmap, clusterProfiler, edgeR, limma, WGCNA, …)
+are exposed as MCP tools and rendered by the user's local **Rscript** to png + pdf.
+
+The Plugin consumes the user's own count/FPKM tables. It does not ship genomes or experimental matrices.
+`tests/data/` is a tiny synthetic `g1`–`g10` table for smoke tests.
+
+MCP **tool names remain `rgraph_*`** (for example `rgraph_volcano`) so existing prompts keep working.
+
+## Try it
+
+```text
+I have gene_count.csv and sample_group.csv. Run DESeq2 for treatment vs control, then draw a
+volcano plot (label top 8 genes, padj < 0.05, |log2FC| > 1) and a clustered heatmap of DEGs.
+```
+
+Expected result: the agent calls `rgraph_env`, then `rgraph_diff(method="deseq2")` and
+`rgraph_volcano` / `rgraph_heatmap`. Output png+pdf paths are returned. DEG calls use **padj**
+by default. If R or a package is missing, the tool returns install commands instead of crashing.
+
+## Requirements
+
+- Python 3.10+ and [uv](https://docs.astral.sh/uv/) on PATH.
+- R with `Rscript` on PATH, or set `RGRAPH_RSCRIPT` to the Rscript executable.
+- Common R packages: ggplot2, pheatmap, edgeR or DESeq2 or limma, clusterProfiler as needed.
+  Missing packages are reported with CRAN/Bioconductor install lines.
+- Windows, macOS, and Linux.
+
+## Data and network
+
+- Default analyses are local: user CSVs in, png/pdf out. No telemetry.
+- `rgraph_ppi` may contact STRING (`string-db.org`) when the user asks for a PPI edge table.
+- No credentials in the package.
+
+## License
+
+MIT. See [LICENSE](LICENSE). Source: https://github.com/Presisitence/rnaseq-plot-mcp

plugins/Presisitence/rnaseq-plot/mcp.json

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

plugins/Presisitence/rnaseq-plot/plugin.json

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+{
+  "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+  "name": "rnaseq-plot",
+  "version": "0.1.1",
+  "description": "RNA-seq downstream plotting via local Rscript: DESeq2/edgeR/limma, volcano, heatmap, GSEA, WGCNA (png+pdf).",
+  "author": {
+    "name": "Presisitence",
+    "url": "https://github.com/Presisitence"
+  },
+  "homepage": "https://github.com/Presisitence/rnaseq-plot-mcp",
+  "repository": "https://github.com/Presisitence/rnaseq-plot-mcp",
+  "license": "MIT",
+  "keywords": [
+    "minimax-code",
+    "plugin",
+    "mcp",
+    "rnaseq",
+    "deseq2",
+    "volcano",
+    "heatmap",
+    "ggplot2",
+    "wgcna"
+  ]
+}

plugins/Presisitence/rnaseq-plot/pyproject.toml

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+[project]
+name = "rnaseq-plot-mcp"
+version = "0.1.1"
+description = "RNA-seq 下游出图 MCP：把一套 R (ggplot2/pheatmap/clusterProfiler/WGCNA...) 脚本封装为工具，由本机 Rscript 渲染 png+pdf"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "MIT"
+dependencies = [
+    "mcp[cli]>=1.2.0",
+]
+
+[project.scripts]
+rgraph-cli = "rgraph_toolkit.cli:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["rgraph_toolkit"]
+
+[tool.hatch.build.targets.wheel.force-include]
+"rscripts" = "rgraph_toolkit/rscripts"

plugins/Presisitence/rnaseq-plot/rgraph_toolkit/__init__.py

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+"""rgraph_toolkit: 把一套 RNAseq 下游 R 出图脚本参数化封装为 MCP 工具。"""
+from __future__ import annotations
+
+from . import runner
+
+__all__ = ["runner"]

plugins/Presisitence/rnaseq-plot/rgraph_toolkit/cli.py

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+"""命令行自检入口：`rgraph-cli` 检查 R 引擎与关键包是否就绪。"""
+from __future__ import annotations
+
+import sys
+
+from . import runner
+
+_KEY_PKGS = [
+    "ggplot2", "dplyr", "tidyr", "stringr", "pheatmap", "ggrepel",
+    "DESeq2", "edgeR", "limma", "clusterProfiler", "enrichplot",
+    "pathview", "circlize", "ComplexHeatmap", "WGCNA", "VennDiagram",
+    "GSVA", "fgsea", "ggpubr", "patchwork", "reshape2",
+]
+
+
+def main() -> int:
+    rscript = runner.find_rscript()
+    print(f"Rscript: {rscript or '未找到 (设置 RGRAPH_RSCRIPT 或安装 R)'}")
+    print(f"rscripts 目录: {runner.rscripts_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())