mlPEA is a user-friendly and multi-functionality platform specifically tailored to the needs of streamlined processing of m6A-Seq data in a reference genome-free manner. By taking advantage of machine learning (ML) algorithms, mlPEA enhanced the m6A-Seq data analysis by constructing robust computational models for identifying high-quality transcripts and high-confidence m6A-modified regions. mlPEA comprises four functional modules: Data Preprocessing, Transcriptome Construction, m6A Calling, and Functional Exploration.