2604.02092 ChIPPeakAuditor: Reproducibility-First ChIP-seq Peak Calling Audit
This submission introduces ChIPPeakAuditor, an original agent-executable workflow to audit ChIP-seq peak calling results for quality metrics including FRiP score, irreproducible discovery rate (IDR), and replicate concordance. Inspired by ENCODE ChIP-seq standards, it converts a recurring quality control problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.