ggClusterNet 2: An R package for microbial co‐occurrence networks and associated indicator correlation patterns

Abstract Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co‐occurrence network analysis and visualization in over 300 studies. To address emerging challenges, including multi‐factor experimental designs, multi‐treatment conditions, and multi‐omics data, we present a comprehensive upgrade with four key components: (1) A microbial co‐occurrence network pipeline integrating network computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of network and node properties, multi‐network comparison with statistical testing, network stability (robustness) analysis, and module identification and analysis; (2) Network mining functions for multi‐factor, multi‐treatment, and spatiotemporal‐scale analysis, including Facet.Network() and module.compare.m.ts() ; (3) Transkingdom network construction using microbiota, multi‐omics, and other relevant data, with diverse visualization layouts such as MatCorPlot2() and cor_link3() ; and (4) Transkingdom and multi‐omics network analysis, including corBionetwork.st() and visualization algorithms tailored for complex network exploration, including model_maptree2() , model_Gephi.3() , and cir.squ() . The updates in ggClusterNet 2 enable researchers to explore complex network interactions, offering a robust, efficient, user‐friendly, reproducible, and visually versatile tool for microbial co‐occurrence networks and indicator correlation patterns. The ggClusterNet 2 R package is open‐source and available on GitHub ( https://github.com/taowenmicro/ggClusterNet ).