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differential-clip

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

When to use

• computing condition-level changes in RBP binding intensity
• choosing peak-level vs window-level vs crosslink-level testing
• designing replicate experiments
• distinguishing biological binding shifts from technical confounders
• differential CLIP-seq analysis
• testing for condition-level differences in IP enrichment
• using DEWSeq, Flipper, ASpeak, edgeR, or limma-voom

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