ChIPseeker is an R/Bioconductor package designed for annotating, comparing, and visualizing ChIP-seq data. It addresses the limitations of existing tools by providing a comprehensive set of functionalities, including peak annotation with nearest genes and genomic regions, visualization of peak coverage, and comparison of peak profiles. The package supports statistical testing for significant overlap among ChIP-seq datasets, enabling the identification of co-factors and cooperative regulation. ChIPseeker also includes a database of 15,000 bed files from the GEO database, facilitating the comparison of user data with publicly available datasets. The package is freely available under the Artistic-2.0 License and can be accessed through Bioconductor.ChIPseeker is an R/Bioconductor package designed for annotating, comparing, and visualizing ChIP-seq data. It addresses the limitations of existing tools by providing a comprehensive set of functionalities, including peak annotation with nearest genes and genomic regions, visualization of peak coverage, and comparison of peak profiles. The package supports statistical testing for significant overlap among ChIP-seq datasets, enabling the identification of co-factors and cooperative regulation. ChIPseeker also includes a database of 15,000 bed files from the GEO database, facilitating the comparison of user data with publicly available datasets. The package is freely available under the Artistic-2.0 License and can be accessed through Bioconductor.