Analysis code repository for the paper "Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries", published in Genome Biology.

The analysis pipeline runs on Python 3+. Please install the dependencies by running:

pip install -r requirements.txt

To reproduce the figures of the paper, run the following scripts from the root folder of this repository. The scripts have to be run in order. All the figures will be generated and put in the figures/analysis folder.

python src/analysis/ctcf_analysis.py

python src/analysis/boundary_consensus.py

python src/analysis/ctcf_looping.py

python src/analysis/ctcfs_on_tads.py
python src/analysis/directionality.py

python src/analysis/ctcfs_on_genes.py