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.