Bronchoalveolar lavage fluid mNGS DNA and RNA sequencing datasets and analysis script

This repository contains original codes for major analyses in the manuscript 'Multimodal Metagenomic Analysis of Bronchoalveolar Lavage Fluid Enables Differential Diagnosis Between Lung Cancer and Pulmonary Infections'. All data are included in the 'data' directory. In "pipeline" and "machine_learning_scripts" folders, the codes for the major analyses are included. The processed microbiome and host data for all 402 individuals are provided. All data published were accorded to Human Genetic Resources Administration of China regulation and to comply with informed consent.