Introduction | Installation | Quick start - Generate Differential Networks | Key Parameters of get_diffNetworks | Visualization | List All Differential Interactions | Differential Regression Plots | Differential Network Analysis with More Than Two Groups | Feature Selection and Engineering with multiDEGGs in Nested Cross-Validation | Why Nested Cross-Validation for Feature Engineering? | multiDEGGs_filter(): Pure Differential Network-Based Selection | Key Parameters | Usage Examples | Basic Usage: Pairs Only | Including Individual Genes (keep_single_genes = TRUE) | How nfilter works with keep_single_genes | multiDEGGs_combined_filter(): Hybrid Statistical and Network-Based Selection | Dynamic vs. Balanced Selection Modes | Dynamic Selection (dynamic_nfilter = TRUE) | Balanced Selection (dynamic_nfilter = FALSE) | Available Statistical Methods | Practical considerations | Feature Engineering Details | Citation

Feature Selection and Feature Engineering with multiDEGGs in Nested Cross-Validation | Why Nested Cross-Validation for Feature Engineering? | multiDEGGs_filter(): Pure Differential Network-Based Selection | Key Parameters | Usage Examples | Basic Usage: Pairs Only | Including Individual Genes (keep_single_genes = TRUE) | How nfilter works with keep_single_genes | multiDEGGs_combined_filter(): Hybrid Statistical and Network-Based Selection | Dynamic vs. Balanced Selection Modes | Dynamic Selection (dynamic_nfilter = TRUE) | Balanced Selection (dynamic_nfilter = FALSE) | Available Statistical Methods | Practical considerations | Feature Engineering Details | Citation

Introduction | Installation | Quick start - Generate Differential Networks | Key Parameters of get_diffNetworks | Visualization | List All Differential Interactions | Differential Regression Plots | Differential Network Analysis with More Than Two Groups | Custom Reference Network | Citation