R script for co-occurrence network analysis of rumen bacterial ASVs

This repository contains the R script used to construct the co-occurrence network of rumen bacterial ASVs based on Spearman correlations of relative abundances.The analysis identifies significant co-occurring relationships, detects network modules, evaluates module–group associations (LY vs HY), and visualizes the modular structure of the rumen bacterial community.The script was developed for the study: Zheng X., Lai Z., Zhang M., and Mao S. (2025). A functional dichotomy in the rumen microbiome: multi-omics reveal how propionate-driven microbial ecosystems enhance host lactation performance. [Manuscript submitted for publication]. The script uses R (version 4.3.2) and requires the following packages: igraph, DESeq2, Hmisc, ggplot2, dplyr, tidyr, reshape2, psych.Released under CC-BY 4.0 License.