https://github.com/menchelab/apobex
https://github.com/menchelab/apobex
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/menchelab/apobex
- Owner: menchelab
- License: mit
- Created: 2024-04-17T17:26:55.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-06-10T09:50:08.000Z (about 2 years ago)
- Last Synced: 2025-02-05T20:01:55.184Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 6.47 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
```bash
git clone https://github.com/menchelab/apobex.git
```
#### 2. Navigate into the ApobeX directory within the cloned repository
```bash
cd apobex #go into cloned repository
```
#### 3. Install the ApobeX package from the local repository:
```R
library(devtools)
install("ApobeX")
```
#### 4. Load the ApobeX package:
```R
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