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hic-differential

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Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries (delta insulation), and differential loops (diffloop, DiffHiChIP) -- with distance-stratified between-sample normalization, replicate-aware NB-GLM FDR, HiCRep SCC reproducibility gating, and CNV correction for cancer/aneuploid samples. Use when comparing Hi-C between treatment and control, finding differential contacts/compartments/boundaries/loops, normalizing two maps of unequal depth, choosing a replicate-aware test, gating replicates with SCC, or correcting copy-number artifacts before a tumor-vs-normal comparison.

When to use

• comparing Hi-C between treatment and control
• finding differential contacts
• finding differential compartments
• finding differential TAD boundaries
• finding differential loops
• normalizing two maps of unequal depth
• choosing a replicate-aware test
• gating replicates with SCC

When not to use

• pixel-wise log2 subtraction
• using bin-pair tools to find compartment changes

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