Add plugin rnaseq-plot

[Presisitence]

What changes

New Plugin Presisitence/rnaseq-plot — RNA-seq downstream plotting driven by local Rscript (DESeq2/edgeR/limma, volcano, heatmap, GSEA, WGCNA).

Formerly drafted as rgraph; renamed so the catalog name states the job. MCP tool functions stay rgraph_* (for example rgraph_volcano).

Path: plugins/Presisitence/rnaseq-plot. Standalone source: https://github.com/Presisitence/rnaseq-plot-mcp

User value

Given the user's own count/expression tables, MiniMax Code can normalize, call DEGs (padj by default), and write png+pdf figures without reimplementing the plots in Python.

Example prompt:

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: rgraph_env then rgraph_diff(method="deseq2") plus rgraph_volcano / rgraph_heatmap; png+pdf paths returned. Missing R or packages yield install commands, not a crash.

Plugin submission checklist

• Plugin lives at plugins/<github-owner>/<plugin-name>.
• plugin.json name matches the Plugin directory.
• README.md includes a real example prompt and expected result.
• LICENSE and plugin.json declare an open-source license.
• Required executables, accounts, paid services, and supported platforms are disclosed.
• Network destinations and data handled by the plugin are disclosed.
• No credentials, private endpoints, hidden telemetry, installers, symlinks, or native binaries are included.
• Every scaffold placeholder has been replaced.
• Validator accepts this Plugin (validateHostedPluginDirectory).

Dependencies and platforms

• Python 3.10+ and uv on PATH.
• R with Rscript on PATH, or RGRAPH_RSCRIPT pointing at the executable.
• R packages as needed (ggplot2, pheatmap, DESeq2/edgeR/limma, clusterProfiler, …); missing packages are reported with install lines.
• Windows, macOS, Linux.

Network and data behavior

Default analyses are local (user CSVs in, png/pdf out). rgraph_ppi may contact STRING (string-db.org) when requested. No telemetry. tests/data/ is a synthetic g1–g10 table only.

Evidence

validateHostedPluginDirectory plugins/Presisitence/rnaseq-plot
OK Presisitence/rnaseq-plot skills=rnaseq-plot mcp=rnaseq-plot

Manual: stdio MCP uses bare uv + ${PLUGIN_ROOT}; no private data; MIT LICENSE.