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enhancer-gene-linking

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

When to use

• linking distal enhancers to target genes
• choosing between contact-aware and accessibility-only approaches
• validating predictions against CRISPRi-FlowFISH
• building cell-type-specific regulatory maps
• fine-mapping
• therapeutic target discovery
• predicting enhancer-gene regulatory connections from ATAC-seq

When not to use

• tasks not involving enhancer-gene linking
• non-ATAC-seq based regulatory prediction without specified tools

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