Add plugin microbe

[Presisitence]

What changes

New Plugin Presisitence/microbe — 16S/ITS downstream microbiome analysis via local Rscript (alpha/beta diversity, composition, differential abundance, co-occurrence, random forest, taxonomy tree).

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

User value

Given a feature table, taxonomy, and metadata, MiniMax Code can run vegan/DESeq2-style downstream plots and write png+pdf without starting from raw reads.

Example prompt:

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: microbe_env then microbe_alpha, microbe_beta, microbe_composition, microbe_diff, microbe_network; png+pdf paths and key stats returned. Does not run DADA2/QIIME2.

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 TODO has been replaced.
• npm run check validator accepts this Plugin (validateHostedPluginDirectory).

Dependencies and platforms

• Python 3.10+ and uv on PATH.
• R with Rscript on PATH, or MICROBE_RSCRIPT.
• R packages such as vegan, ggplot2, igraph; DESeq2/edgeR optional (tools degrade with install hints).
• Windows, macOS, Linux.

Network and data behavior

Analyses are local on user CSVs. No telemetry. No credentials. tests/prep_test.py writes synthetic OTU-like tables only.

Evidence

validateHostedPluginDirectory plugins/Presisitence/microbe
OK Presisitence/microbe skills=microbe mcp=microbe

Manual: stdio MCP uses bare uv + ${PLUGIN_ROOT}; MIT LICENSE; no private 16S data shipped.