domains / families / science / differential-binding

differential-binding

separate

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

When to use

• comparing ChIP-seq binding between experimental conditions
• choosing normalization for global vs local changes
• integrating spike-in data
• reconciling DiffBind/DESeq2 disagreement
• identifying regions where IP signal changes significantly
• accounting for sequencing depth, composition bias, trended biases, and global shifts

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