This code is associated with the paper from Liu et al., "A large accessory protein interactome is rewired across environments". eLife, 2020. http://doi.org/10.7554/eLife.62365

PPiSeq

Code for the analysis of PPiSeq data from "A large accessory protein interactome is rewired across environments"

Analyses for Figures 1, 2, 3, 4A-C, 5, and Supplementary Figures S1-13

There is a script for each figure panel (e.g. Figure1A). To run the code, please download the addtional datasets (Mendeley Data, https://data.mendeley.com/datasets/9ygwhk5cs3/2), and change the directory in the script accordingly. You can find explanations for some important datasets in the Read_me.txt in the corresponding directory.

Analyses for Figure 4D-F, 6, and Supplementary Figure S14

To replicate these, or extend the analyses, change into that subtree directory. Then, consult that README.md file for instructions on how to download the data archive, extract it, and launch the analysis pipeline.