Raw data and code for Kamrad et al (2025) "Impact of drugs and environmental contaminants on amine production by gut bacteria"

This repository contains raw data, code and analyses outputs. Analyses were performed in python using jupyter notebooks, in particular: 20241104_raw_data_qc_and_hitCalling.ipynb - Initial processing of the LC-MS results of the main screen, including quality control and hit calling. 20241105_intregated_analysis_focused.ipynb - Downstream analysis of the main screen to generate the plots shown in the publication. 20241104_OD_analysis.ipynb - Analysis of the growth data of the main screen. The other files and folders are inputs and outputs of these jupyter notebooks. The file 20241117_longData_withOD.csv contains all individual recorded datapoints of the experiment in long format. The folder dose-response_screen contains all data and notebooks associated with the dose response screen.