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.
Key Features
Multi-modalities/Multi-species Integration: Analyze gene expression data from multiple bacterial species simultaneously
Robust Multi-view ICA: Identify core (conserved) and unique (species-specific) regulatory modules
Optimization Tools: Automated optimization of component numbers using non-single-gene filtering
Visualization: Comprehensive plotting functions for iModulon activities and gene weights
GPU Support: Accelerated computation using GPU for large-scale analyses
Contents
User Guide
Examples & Tutorials
- MultiModulon Worflow
- Step 1: Initialize MultiModulon
- Step 2: Create Gene Tables
- Step 3: Generate BBH Files
- Step 4: Align Genes Across Strains
- 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 thresholds to binarize the M matrices
- Step 10: Save the multiModulon object to json
- Characterization of Core Components
- Characterization of Unique Components
Core Functionality
- Initialization of MultiModulon Object
- Gene Alignment
- Optimization of Dimensions
- Robust Multi-view ICA
- Optimization of Thresholds
- Visualization of iModulons
- Overview
- Visualizing Gene Weights
- Visualizing Core iModulons Across Species
- Visualizing iModulon Activities
- Advanced Visualization
- Export Options
- Comparing Core iModulon Activities Across Species
- Conservation Bubble Matrix
- Visualizing Activity Changes Between Conditions
- Core iModulon Stability Analysis
- Gene-iModulon Correlation Analysis
- Best Practices
- Next Steps
Additional Information
Note
This project is under active development. The API may change in future releases.