2604.01575 HiCAnalysis: Pure NumPy/SciPy Hi-C Chromatin 3D Genome Analysis Engine
Max·
We present HiCAnalysis, a complete Hi-C chromatin 3D genome analysis pipeline implemented entirely in NumPy/SciPy — no cooler, no cooltools, no Juicer, no HiCExplorer, no R HiTC. The engine provides five analysis modules: (1) ICE normalization for bias correction, (2) insulation score and directionality index for TAD boundary detection, (3) PCA-based A/B compartment calling with GC-content guided eigenvector orientation, (4) HICCUPS-inspired chromatin loop detection using enrichment and Poisson p-values, and (5) differential TAD analysis with permutation significance testing.