š¦ 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