E-P-INAnalyzer

E-P-INAnalyzer is a Python-based toolkit for understanding enhancer-promoter interaction networks from RNA-Seq, ATAC-Seq, and ChIP-Seq datasets. E-P-INAnalzyer allows researchers to reveal substructures, integrate transcription factors, locate disease-associated variation, and perform enrichment analyses on enhancer-promoter interaction networks.

E-P-INAnalzyer can be installed using this GitHub repository:

# Clone E-P-INAnalyzer’ GitHub
git clone https://github.com/KreimerLab/E-P-INAnalyzer.git

# Navigate to E-P-INAnalyzer
cd E-P-INAnalyzer/E-P-INAnalyzer

We provided a singular computational framework for a task that depends on Python, R, and Bash. Inputting appropriate datasets, which can be found in GitHub's E-P-INs section, will allow these tasks to run in sequence.

Preprint: DeGroat, W. et al. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. 2024.05.22.595375 Preprint at https://doi.org/10.1101/2024.05.22.595375 (2024).