Introduction | Installation requirements | Correlation guided Network integration (CoNI) | Run CoNI | Load data | Create networks | Basic network statistics | Clustering options in igraph | Community structure detecting based on the leading eigenvector (Spectral community) | Community structure via greedy optimization of modularity | Local controlling genes (local controlling edge features) | Genes by confounding magnitude | Bipartite graphs | Comparison between treatments | Triplet comparison | Compare metabolite-pair classes | Compare metabolite classes per gene