Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with urinary tract infections.

Outline:

• All the relevant data files can be found in data folder. If moving files around, make sure the config file that comes with each figure folder has correct paths

• analysis folder contains a folder for each of the figures:

  • Figure 1
  • Figure 2 and Figure 3
  • Figure 4

• General settings for each of the jupyter notebooks can be found in settings.py