Changelog

Version 1.0.0

First published version with full tutorial.

Highlights:

  • End-to-end MultiModulon workflow tutorial

  • Core component characterization tutorial

  • Unique component characterization tutorial

  • Multi-species/strain expression analysis with multi-view ICA

  • BBH-based ortholog detection and gene alignment

  • Core/unique component optimization with non-single-gene filtering

  • Robust multi-view ICA and threshold optimization

  • Visualization and interpretation utilities for iModulons

Version 0.2.0

Visualization:

  • view_iModulon_weights - Gene weight plots per species

  • view_iModulon_activities - Activity bar plots across samples

  • view_iModulon_genes - Gene membership table per component

  • view_core_iModulon_weights - Core component weights across species

  • compare_core_iModulon - Gene membership comparison heatmap

  • compare_core_iModulon_activity - Cross-species activity comparison

  • plot_iM_conservation_bubble_matrix - Conservation bubble matrix summary

  • show_iModulon_activity_change - Condition-vs-condition activity scatter

  • show_gene_iModulon_correlation - Gene expression vs activity correlation

  • core_iModulon_stability - Cross-species stability scores

Version 0.1.0

Initial release of MultiModulon package.

Features:

  • Multi-species/strain expression analysis using multi-view ICA

  • Bidirectional Best Hits (BBH) for ortholog detection

  • Union-Find based gene alignment across species

  • Robust multi-view ICA with clustering

  • Automated optimization of component numbers

  • GPU acceleration support

  • JSON-based data persistence

Core Functionality:

  • MultiModulon class for managing multi-species analysis

  • SpeciesData container for individual species data

  • BBH generation using containerized BLAST

  • Gene alignment with customizable thresholds

  • Multi-view ICA with PyTorch backend

  • Single-gene component filtering

  • Otsu’s method for threshold optimization

Optimization:

  • Single-gene filter-based optimization workflow

  • Separate optimization for core and unique components

  • Cross-validation support

  • Automated parameter selection

Utilities:

  • GFF parsing and gene table creation

  • eggNOG annotation integration

  • FASTA sequence extraction

  • Data validation and quality control

Documentation:

  • Comprehensive API documentation

  • Step-by-step tutorials

  • Example workflows