README

Author: Michał Denkiewicz (michal.denkiewicz@pw.edu.pl)

This repository is a supplement to the "Intrinsic linking of chromatin fiber in human cells" manuscript. It contains the code for all of the statistical analyses, plots and visualization performed for this manuscript.

The code was tested on Python 3.10.14, to install the required packages use:

pip install -r requirements.txt

Analysis code

The Following notebooks contain the code for data analysis of the raw cKNOTs results.

• data_consolidation.ipynb - Noteboook used to create intermediate files before the analysis.
• analysis.ipynb - Contains the statistical analyses used in the manuscript.
• graph_visualization.ipynb - A Jupyter notebook that alolows to visualize a single CCD as a graph and a 3D model.
• batch_models_analysis.ipynb - Analyses the linking in batches of 3D models.

Usage: Simply exectue all cells in the notebook.

Utilities

• datasources.py - Utility to load data from multiple files with a particular naming pattern into a Pandas DataFrame.
• knots_tools.py - Code closely related to operating on cKONTs data.
• modvis.py - Package gathers visualization code, as well as provides easy way to launch 3D modeling a obtain results.
• read_chiadrop.py - Utilities for reading ChIA-Drop data described in the manuscript.
• batch_models.py - Standalone python program that runs batches of 3D modeling of a single CCD.
• show_pyvista_model.py - Utility to show a 3D model in pyvista outside jupyter.

Bash scripts

The bash scripts realte to running of Spring Model modeling software.