ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data

Chromatin profiling technologies such as CUT&Tag and ChIP-seq have greatly advanced epigenomic research by enabling genome-wide mapping of histone modifications and transcription factor binding, providing key insights into gene regulation, cellular differentiation, and disease mechanisms. However, interpreting these datasets remains difficult for many researchers due to the technical expertise required for data processing and analysis. To address this limitation, we developed ChromTag, an interactive web-based application built with R Shiny for the comprehensive exploration and visualization of CUT&Tag and other epigenomic profiling datasets. Using a modular workflow, ChromTag performs differential peak detection, assigns peaks to nearby genes based on user-defined genomic windows, and supports ORA-based GO and KEGG enrichment analysis and preranked GSEA using gene-level summaries derived from peak annotation. The platform separates upregulated and downregulated regions to distinguish activated from repressed regulatory pathways and incorporates motif enrichment analysis to highlight transcription factors that may cooperate with chromatin modifications to influence gene expression. ChromTag currently supports human, mouse, and Drosophila datasets, and provides extensive visualization options such as volcano plots, PCA, heatmaps, and genomic peak profiles. By bridging preprocessed peak count matrices with interactive visualization and exploratory functional interpretation, ChromTag provides a practical and accessible downstream analysis solution for chromatin profiling data.