A central hub for convergence: Multi-layer genomic networks reveal lineage-specific plasmid compatibility driving hypervirulence and carbapenem resistance in ST11 Klebsiella pneumoniae

This repository contains the complete data and analysis scripts underlying the figures and supplementary figures of the manuscript: "A central hub for convergence: Multi-layer genomic networks reveal lineage-specific plasmid compatibility driving hypervirulence and carbapenem resistance in ST11 Klebsiella pneumoniae" The dataset includes: Curated tables of core genome orthologs, plasmid replicon types, prophage regions, and resistance/virulence gene profiles. Sequence-similarity network files (e.g., edge lists and node attributes) used for plasmid and prophage community detection. Reproducible R/Python scripts for generating all main and supplementary figures, including network visualizations, synteny plots, and statistical enrichment analyses. All scripts are documented to enable full reproduction of the multi-layer population genomic framework, from raw data processing to final figure generation. The data are provided in open formats (CSV, TSV, GFF, FASTA, and GraphML) to facilitate reuse and comparative studies. For any questions regarding the data or code, please contact the corresponding authors.