Welcome to MultiModulon’s documentation!
MultiModulon is a Python package for an integrative multi-species/multi-strains/multi-modalities analysis framework. It enables the identification of conserved and species-specific regulatory modules across multiple bacterial strains or species.
Note
This project is under active development. The API may change in future releases.
Key Features
Multi-species Integration: Analyze gene expression data from multiple bacterial species simultaneously
Multi-view ICA: Identify core (conserved) and unique (species-specific) regulatory modules
Optimization Tools: Automated optimization of component numbers using multiple metrics
Visualization: Comprehensive plotting functions for iModulon activities and gene weights
GPU Support: Accelerated computation using GPU for large-scale analyses
Contents
User Guide
Core Functionality
Examples & Tutorials
- Basic Workflow
- Step 1: Initialize MultiModulon Object
- Step 2: Generate BBH Files
- Step 3: Align Genes Across Strains
- Step 4: Create Gene Tables
- Step 5: Generate Aligned Expression Matrices
- Step 6: Optimize Number of Core Components
- Step 7: Optimize Number of Unique Components
- Step 8: Run Robust Multi-view ICA
- Step 9: Optimize M Matrix Thresholds
- Step 10: Save Results
- Summary
- Characterization and Visualization
Additional Information