This repository contains data and computer codes for main bioinformatic analyses of the manuscript (Yan et al. 2022, Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions, In Press, Nature Microbiology).

• 1-Metagenome, which contains the commands and scripts to process metagenomic data to generate taxonomic and functional profiles for this study.
• 2-Transcriptome, which contains the commands and scripts to process host transcriptomic to generate gene expression table for this study.
• 3-Metabolome and Proteome, which describes the processes to generate metabolomic data and sputum and serum proteomic data for this study.
• 4-Multi-omic Integration, which contains the original scripts and datasets for downstream multi-omic data analyses for this study.
• 5-Datasets, which contains clinical metadata table and the processed (original and dimensionality reduced) multi-omic data tables.
• 6-Figure scripts, which contains the scripts and datasets for the main and supplementary figures for this study.