Key features of cross-domain analysis | Example with custom data | Interpretation

Installation | Available vignettes | Basic Usage | Analysis of American Gut data | Next steps

Key differences from standard SPIEC-EASI

Windows-specific considerations | Option 1: Use batch mode with snow | Option 2: Use serial processing | Option 3: Use batch mode | Batch Mode | Performance comparison | Key parameters | Platform-specific recommendations | Unix-like systems (Linux, macOS): | Windows systems:

Common issues and solutions | 1. Empty networks | 2. Very dense networks | 3. Computational issues | 4. Windows parallel processing issues | 5. Convergence issues | 6. Memory issues | Platform-specific considerations | Windows users: | Unix-like systems (Linux, macOS): | Diagnostic functions | Parameter tuning guidelines | For small datasets (< 100 samples, < 50 taxa): | For medium datasets (100-1000 samples, 50-200 taxa): | For large datasets (> 1000 samples, > 200 taxa): | Windows-specific recommendations:

Learning Graphs with a few hubs | Augmented AGNES | References