ElectricColiModelingClean.m contains scripts for flux balance analysis of the strains and conditions used in this project. These scripts require MATLAB, the COBRA toolbox (https://opencobra.github.io/cobratoolbox/stable/index.html), and a convex solver such as Gurobi (https://www.gurobi.com/) to run.

A preprint of this work is available here: https://www.biorxiv.org/content/10.1101/2024.05.30.596743v1.full

Unzip all the zipped files in the transcriptomics/models folder before proceeding to run the notebooks

Use requrements_deseq.txt to set up a virtual environment ONLY for the DEGs.ipynb notebook. Use requirements_1.txt to set up a virtual environment to run the other notebooks. Notebook descriptions:

1. DEGs.ipynb contains code to perform differential gene expression analysis for a pair of samples and get enriched treemaps
2. DiMA_and_Treemaps.ipynb contains code to perform differential imodulon activity analysis for a pair of samples and makes enriched treemaps of imodulon functionality
3. fig5.ipynb contains all the code to generate the figures used in figure 5
4. fig6.ipynb contains all the code to generate the figures used in figure 6