ChIP-seq Histone Mark Analysis Pipeline
A pure-Python computational engine for histone modification analysis from ChIP-seq data.
- Peak calling (fold-enrichment over input, Poisson p-value, BH FDR)
- Bivalent domain detection (H3K4me3 + H3K27me3 co-occurrence)
- 5-state chromatin segmentation (active/poised/repressed/heterochromatin/quiescent)
- Histone mark correlation matrix
- Enhancer/promoter classification from mark combinations
- 200 genomic bins × 5 histone marks, 2 cell types
- Total peaks (Cell A): 66, (Cell B): 68
- Bivalent domains: A=1, B=4
- H3K4me3-H3K27ac correlation: 0.503
pip install numpy scipy matplotlib
python histone_modification_engine.pyhistone-modification chip-seq-peak h3k27ac h3k4me3 bivalent-chromatin chromatin-state