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motif-deviation

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

When to use

• identifying TF motifs whose accessibility correlates with conditions
• computing per-sample motif z-scores
• comparing to ArchR / Signac equivalents
• distinguishing motif-accessibility signal from per-site footprinting
• per-cell TF activity in scATAC
• Which TF families distinguish my cell clusters?

When not to use

• per-site footprinting
• Is THIS specific motif site bound by a TF?
• Per-cell TF binding at specific sites
• Differential bound vs unbound between conditions
• TF activity inference requiring paired RNA-seq

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