Metagenomics Functional Analysis

Overview

This repository contains metagenomic and microbiome functional profiling workflows developed in R for comparative microbial community analyses.

The analyses include:

• Host read filtering assessment
• Alpha diversity analysis
• Taxonomic profiling
• Shared and unique taxa analysis
• KEGG functional annotation
• Statistical visualisation

Workflow Overview

Raw sequencing counts
        ↓
Metadata integration
        ↓
Taxonomic abundance processing
        ↓
Alpha diversity analysis
        ↓
Taxonomic profiling
        ↓
Shared vs unique taxa analysis
        ↓
KEGG functional profiling
        ↓
Statistical summaries
        ↓
Visualisation and reporting

Tools & Packages

• R
• phyloseq
• DESeq2
• vegan
• ggplot2
• KEGGREST
• tidyverse
• pheatmap

Skills Demonstrated

• Metagenomics analysis
• Functional microbiome profiling
• Statistical modelling
• Diversity analysis
• Data visualisation
• Reproducible R workflows

Repository Structure

scripts/        R analysis scripts
figures/        Example visualisations
tables/         Summary output tables
workflow/       Pipeline diagrams
notebooks/      RMarkdown workflows
docs/           Methodology documentation
environment/    Package requirements

Notes

This repository was reconstructed and modularised from postgraduate bioinformatics coursework to demonstrate reproducible metagenomics analysis workflows.