Skip to content

Latest commit

 

History

History
18 lines (15 loc) · 479 Bytes

README.md

File metadata and controls

18 lines (15 loc) · 479 Bytes

🦠 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