CexoR

CexoR analyzes replicated ChIP-exo BAM alignments to identify and rank strand-specific protein-DNA binding sites.

Key Features:

• Strand-Specific Analysis: Uses the cumulative Skellam distribution function from the skellam package to detect significant normalized count differences between opposing DNA strands at each peak-pair.
• Peak-Pair Identification: Identifies peak-pairs by calculating probabilities with the Skellam distribution, modeling the cross-correlation of two Poisson distributions to detect consecutive punctate read enrichment on Watson-and-Crick strands.
• Irreproducible Discovery Rate (IDR): Estimates the irreproducible discovery rate for overlapping peak-pairs across biological replicates using the idr package to rank reproducible events.
• Output Format: Reports results in BED format files for downstream genomic analyses.

Scientific Applications:

• High-resolution mapping of protein-DNA interactions: Enables precise localization of protein-binding events from ChIP-exo data by exploiting strand-specific exonuclease digestion signals.
• Extension to related protocols: Can be applied to similar high-resolution ChIP protocols such as ChIP-nexus for strand-specific peak-pair detection.

Methodology:

Accepts replicated ChIP-exo data in BAM alignment format; applies the cumulative Skellam distribution (skellam package) to detect normalized strand-count differences and to compute peak-pair probabilities modeling two Poisson distributions; estimates reproducibility across replicates with the idr package; outputs results in BED format.