This repository contains code and data to reproduce analyses for the manuscript Metabolic modeling enables personalized Clostridioides difficile engraftment predictions in the human gut.
- Data tables containing processed genus level composition predicted growth rates and fluxes can be found the data folder, tables exceeding 25 MB can be founder here: 10.5281/zenodo.13315667.
- Scripts used to process raw sequencing data with QIIME2 can be found in the scripts/QIIME2 folder
- Scripts used to generate predicted growth rates and fluxes can be found in the scripts/Micom folder
- Jupyter notebooks used for data analysis and the production of figures in the manuscript can be found in the notebooks folder
- The conda environemnt used in the metabolic modeling analyses can be reproduced using the micom.yaml file and the command
conda env create -f micom.yaml