StrepSuis_Suite

Comprehensive bioinformatics analysis suite for Streptococcus suis genomics

Integrated tools for antimicrobial resistance, virulence factors, and phylogenetic analysis

View on GitHub Try in Colab Launch in Binder

Quick Access for Researchers

Documentation

Complete guides and tutorials

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Example Data

Sample datasets for testing

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Example Results

Pre-generated analysis outputs

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Available Analysis Tools

StrepSuis-AMRVirKM Production Ready

K-Modes Clustering of Antimicrobial Resistance and Virulence Profiles in Streptococcus suis

Automatic optimal cluster number selection
Multiple Correspondence Analysis (MCA)
Bootstrap confidence intervals
Feature importance ranking

Use when: Identifying strain groups based on resistance patterns

Run in Colab Learn More View Example Results

StrepSuis-AMRPat Production Ready

Automated Detection of Antimicrobial Resistance Patterns in Streptococcus suis

Multi-drug resistance pattern analysis with hybrid networks

Customizable MDR threshold
Bootstrap prevalence estimation
Association rule mining
Hybrid co-resistance network visualization

Use when: Analyzing antibiotic resistance patterns and MDR strains

Run in Colab Learn More View Example Results

StrepSuis-GenPhenNet Production Ready

Network-Based Integration of Genome–Phenome Data in Streptococcus suis

Chi-square and Fisher exact tests
Information theory metrics (entropy, Cramér's V)
3D network visualization
Community detection and hub identification

Use when: Finding feature correlations and relationship networks

Run in Colab Learn More View Example Results

StrepSuis-PhyloTrait Production Ready

Integrated Phylogenetic and Binary Trait Analysis of Antimicrobial Resistance and Virulence in Streptococcus suis

Tree-aware clustering methods
Faith's Phylogenetic Diversity
UMAP dimensionality reduction
Trait-phylogeny associations

Use when: Analyzing phylogenetic relationships and evolution

Run in Colab Learn More View Example Results

StrepSuis-GenPhen Production Ready

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

Ensemble clustering with fallback
Chi-square trait associations
Random Forest feature importance
Comprehensive trait profiling

Use when: Characterizing Streptococcus suis strains

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Key Features

Production Ready

All tools are fully functional and validated for scientific publications

Publication Quality

High-resolution charts (150+ DPI) and professional reports

Reproducible

Fixed random seeds and documented parameters ensure reproducibility

Multiple Formats

HTML, Excel, and PNG outputs for different use cases