NER and 3D Genome Analysis

This repository contains analysis code for the paper "RNAPII and NER stall loop extrusion at UV lesions, shaping the 3D genome during repair".

All analyses were performed on an Arch Linux system. To facilitate reproducibility of the analyses and manuscript figures, the corresponding code has been deposited primarily as Python-based Jupyter notebooks, with cell outputs preserved, including the generated figures. Additional shell and R scripts used in the analysis are also provided.

Please see the other repositories related to this study for additional research code:

• 1D Simulation Engine
• PHACE-MP

Package Management

Python packages were managed using uv. The required dependencies can be installed using the following command:

uv sync --dev

R packages were managed using renv. The package versions used in this analysis are recorded in r_env/renv.lock.

To install the required R packages and activate the R environment, navigate to the r_env/ directory and start R:

cd r_env
R

Then restore the package environment from the lockfile:

renv::restore()

After restoration, the renv environment will be loaded automatically whenever R is started from the r_env/ directory.

Repository structure

• src/ggner_3d/: Contains helper modules for the analysis, including; data loading, processing, and plotting functions.
• 3d_prep/: Contains scripts for identifying architectural features on contact maps, including; expected frequency calculation, compartment identification, insulation based TAD calling, and loop calling.
• notebooks/: Contains Jupyter notebooks for each analysis step, with outputs and figures included.
• r_env/: Contains the R environment and package lockfile for reproducibility.
• scripts/: Contains additional shell and R scripts used in the analysis.

Todo:

• Prior to publication, we will reorganize the repository, remove temporary and redundant files, and provide a more detailed overview of its structure, including the purpose of each script and notebook.

Data availability

Please see the data availability statement in the manuscript for details on how to access the datasets used in this study.

Contact

Please email vogulcan@sabanciuniv.edu or raise an issue in the github repository with any questions about installation or usage.