High-precision Detection of RNA Editing Sites using Calibrated Differential RNA Editing Scanner.

Accurate delineation of RNA editing remains technically challenging because genuine post‑transcriptional alterations must be distinguished from genomic variants and sequencing artifacts. This difficulty is especially marked for cytidine‑to‑uridine editing catalyzed by APOBEC enzymes, where intermixed DNA and RNA changes obscure the true editing signal. The Calibrated Differential RNA Editing Scanner (CADRES) provides a structured computational framework to address these limitations through integrated DNA-RNA variant interrogation and targeted preservation of authentic editing signatures. This protocol presents the CADRES workflow, including data preparation, joint RNA‑variant calling, signal-preserving base-quality recalibration, artifact filtering, and differential assessment of RNA editing between experimental conditions. CADRES supports paired RNA‑seq and whole‑genome or whole‑exome sequencing with biological replication.  A multi-stage filtering strategy, including homopolymer removal and PBLAT-based paralogue screening, systematically reduces false positives while preserving low-frequency editing events. By combining calibration with replicate-aware modeling, CADRES increases the precision and reproducibility of RNA editing analysis, enabling interrogation of editing dynamics across diverse biological contexts. Compared with established methods, CADRES is designed to improve precision in RNA editing detection, particularly for APOBEC-mediated C-to-U events.