ChromatinAccessibilityEngine

ATAC-seq Chromatin Accessibility Analysis Pipeline

A pure-Python pipeline for ATAC-seq analysis including peak calling, NFR classification, TF footprinting, and differential accessibility.

Features

• Peak calling (MACS2-style: local lambda, Poisson test, BH FDR)
• Nucleosome-free region (NFR) vs mono-nucleosomal peak classification
• TF footprinting (Tn5 insertion bias correction, HINT-style)
• Differential accessibility (edgeR-style NB)
• Cell-type-specific accessible regions

Results

• 50 samples × 50,000 peaks, 3 cell types
• Called peaks (FDR<0.05): 15,143
• NFR peaks (<150bp): 22,500 (45%)
• Differential peaks (A vs B): 5,000
• Mean FRiP score: 0.565

Usage

pip install numpy scipy matplotlib
python chromatin_accessibility_engine.py

Tags

chromatin-accessibility atac-seq nucleosome footprinting open-chromatin nfr