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co-accessibility

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Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

When to use

• linking enhancer accessibility to promoter accessibility
• identifying enhancer-gene pairs from chromatin alone
• running gene-regulatory inference combining ATAC + RNA
• comparing predicted regulatory contacts against Hi-C/Micro-C ground truth

When not to use

• 3D physical contacts that don't vary in accessibility
• trans-chromosomal interactions
• constitutive structural contacts
• developmental contacts that opened before scATAC sample
• hub enhancers that contact many distal targets

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