Abstract Epigenome profiling techniques such as ChIP-seq and ATAC-seq have revolutionized our understanding of gene expression regulation in tissue development and disease progression. However, increasing amount of ChIP/ATAC-seq data poses challenges in computational resources, and the absence of systematic tools for epigenomic analysis underscores the necessity for an efficient analysis platform. To address these issues, we developed the Epigenomic Analysis Platform (EAP, https://www.biosino.org/epigenetics ), a scalable cloud-based tool that efficiently analyzes large-scale ChIP/ATAC-seq data sets. EAP employs advanced computational algorithms to derive biologically meaningful insights from heterogeneous datasets and automatically generates publication-ready figures and tabular results, enabling comprehensive epigenomic analysis and data mining in areas like cancer subtyping and therapeutic target discovery.

EAP: a versatile cloud-based platform for comprehensive and interactive analysis of large-scale ChIP/ATAC-seq data sets