m6AnetAnalyzer: an R toolkit for post-processing of m6A sites detected by m6Anet

m6AnetAnalyzer is an R package that streamlines post-processing and interpretation of site-level m6A predictions from m6Anet. It summarizes m6A distributions across transcripts, genes, biotypes, and transcript regions, and enables functional annotation using user-provided BED files or built-in datasets, including RNA-binding proteins and SNPs. Condition-specific changes in m6A methylation are quantified using the log2-transformed weighted modification ratio, with statistical tests applied when appropriate to identify significant differential methylation. By integrating differential gene expression data, m6AnetAnalyzer links methylation changes with expression differences, offering biotype- and region-specific insights into how m6A localization patterns relate to transcriptional regulation. Availability  and implementation m6AnetAnalyzer is freely available at https://github.com/hannalee809/m6AnetAnalyzer. It is compatible with Linux, macOS, and Windows platforms. Detailed installation instructions, example input and output files, and a step-by-step analysis workflow are provided in the package vignette.