🦠 Amplicon 16S qiime2.sh Preprocess Quality control & filtering Assign taxonomy Diversity analysis Phylogenetic tree Create visualizations R - qiimer2, phyloseq & metagenomeSeq Sample composition plots Alpha & Beta diversity Differential abundance analysis (for zero inflated data) Python - Microbiome gene set enrichment Microbiome set enrichment analysis with MSEA Pathways enrichment analysis with GSEApy