Code and data for the preprint "Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung". Metagenomic analysis - uses `targets` (workflow manager) and `renv` (environment manager) R packages. - calling `targets::tar_make()`, once the environment is configured using renv and a separate project has been created (with the exact file structure including the data), should run the entire pipeline, creating a _targets folder with all the .rds files - independent objects can be explored using `targets::tar_load(obj)` or `targets::tar_read(plot)` Targets user manual for more information. Preprocessing/QC scripts can be provided upon reasonable request.