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Analysis for amplicon data
License: MIT License
Shell 2.74%
R 9.52%
Jupyter Notebook 87.74%
amplicon16s's Introduction
- Preprocess
- Quality control & filtering
- Assign taxonomy
- Diversity analysis
- Phylogenetic tree
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
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