apobex

This repository contains all data and code to analyze and visualize the mutational data presented in: "Ubiquitin E3 ligases UBR4, UBR5 and HUWE1 protect human genome integrity by targeting cancer-associated APOBEC3 deaminases for degradation" link to preprint: https://www.biorxiv.org/content/biorxiv/early/2024/04/26/2024.04.23.590688.full.pdf

Installation instructions

Installation time 1 minute

1. clone the GitHub repository:

git clone https://github.com/menchelab/apobex.git

2. Navigate into the ApobeX directory within the cloned repository

cd apobex #go into cloned repository

3. Install the ApobeX package from the local repository:

library(devtools)
install("ApobeX")

4. Load the ApobeX package:

library(ApobeX)

Analysis

run notbook ../analysis/bootstrapped_background_correction.ipynb

Plotting

figures

run notebook ../plotting/notbooks/3_apobex_plotting_refitting.ipynb

signature presence test

run norebook ../plotting/notbooks/3_apobex_msigact.ipynb