StrepSuis-GenPhen

An Interactive Platform for Integrated Genomic–Phenotypic Analysis in Streptococcus suis

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Overview

The StrepSuis-GenPhen module is an interactive platform specifically designed for comprehensive integrated genomic-phenotypic characterization of Streptococcus suis strains. It combines phylogenetic clustering with extensive trait profiling to provide detailed insights into strain diversity, antimicrobial resistance, and virulence potential.

Key Features

  • Ensemble Clustering: Multiple algorithms with intelligent fallback strategies
  • Comprehensive Trait Profiling: Chi-square, log-odds, Random Forest importance
  • Association Rules: Apriori mining for trait co-occurrence patterns
  • MCA Visualization: Multiple Correspondence Analysis for categorical data
  • Bootstrap Validation: Robust confidence assessment
  • Interactive Reports: Bootstrap 5 UI with CSV export functionality

When to Use

Use this tool when you want to:

  • Characterize S. suis strain collections
  • Identify virulence factor patterns specific to S. suis
  • Analyze phylogenetic-trait relationships in S. suis
  • Perform comprehensive integrative analysis

Input Files Required

  • tree.newick - Phylogenetic tree (Newick format)
  • MIC.csv - Minimum Inhibitory Concentrations
  • AMR_genes.csv - Antimicrobial resistance genes
  • Virulence.csv - Virulence factors (S. suis specific)

Output Files

  • HTML Report: Comprehensive interactive dashboard with all analyses
  • Excel Workbook: Multi-sheet with cluster assignments, trait profiles, associations
  • PNG Charts: Phylogenetic trees, MCA plots, trait heatmaps
  • CSV Exports: All data tables for further analysis

Statistical Methods

  • Ensemble phylogenetic clustering (TreeCluster, PhyloHMM)
  • Chi-square tests with FDR correction
  • Log-odds ratio calculations for effect sizes
  • Random Forest feature importance
  • Multiple Correspondence Analysis (MCA)
  • Apriori association rule mining
  • Bootstrap confidence intervals

Quick Start

Option 1: Google Colab (Recommended)

Run in Colab

Option 2: Local Installation

git clone https://github.com/MK-vet/MKrep.git
cd MKrep
pip install -r requirements.txt
python StrepSuisPhyloCluster_2025_08_11.py

Option 3: CLI

mkrep-strepsuis --tree tree.newick --data-dir ./data --output ./results

Quick Links

Run in Colab View Example Results Download Demo Data View Source Code

Parameters

Bootstrap 500
FDR Alpha 0.05
Min Support 0.1
Random Seed 42

Runtime

10-20 minutes

Most comprehensive analysis pipeline

Documentation