Description
Use when the user has a 16S or ITS feature table plus taxonomy and metadata and needs alpha/beta diversity, composition bars, differential abundance, co-occurrence networks, random-forest biomarkers, or a taxonomy tree. Drive the microbe MCP tools with local Rscript.
SKILL.md
microbe
Use the microbe MCP tools. Do not reimplement vegan/DESeq2 plots in Python.
Typical order
microbe_envmicrobe_alpha,microbe_betamicrobe_composition,microbe_diffmicrobe_network,microbe_rf,microbe_corr,microbe_treeas requested
Expected columns: feature_id + sample counts; taxonomy ranks or a QIIME semicolon string; sample_name + group.
Missing R or packages: return the tool's repair command. This Plugin does not go from raw reads to ASVs.
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