ChIPseeker is an R/Bioconductor package for ChIP peak annotation, comparison, and visualization. It supports annotating ChIP peaks, visualizing peak coverage over chromosomes and binding profiles to TSS regions, and comparing peak profiles and annotations. It also allows evaluating significant overlap among ChIP-seq datasets. ChIPseeker contains 15,000 bed files from the GEO database, enabling users to compare their data with public datasets to identify co-regulated genes or transcription factor complexes. ChIPseeker provides functions for annotating peaks with nearest genes and genomic regions, including details about exons and introns. It includes visualization tools such as plotAnnoBar, plotAnnoPie, vennpie, and plotDistToTSS. It supports annotation of ChIP-seq data across various species using TxDb objects generated from UCSC, BioMart, or GFF/GTF files. For functional enrichment analysis, it integrates with Bioconductor packages like clusterProfiler, DOSE, and ReactomePA to identify biological themes through Gene Ontology, KEGG, Disease Ontology, and Reactome Pathway. ChIPseeker visualizes peak locations and intensities across the genome and provides tools for comparing peak profiles between experiments. It includes vennplot for calculating and visualizing peak overlaps, and enrichPeakOverlap for statistically rigorous comparisons of ChIP-seq datasets. It also allows testing overlap significance among datasets from different genomes or species. ChIPseeker incorporates GEO datasets, enabling users to compare their data with public datasets to infer co-factors. The package is released under the Artistic-2.0 License and is freely available through Bioconductor. It is supported by the National Natural Science Foundation of China and the Guangdong Natural Science Research Grant.ChIPseeker is an R/Bioconductor package for ChIP peak annotation, comparison, and visualization. It supports annotating ChIP peaks, visualizing peak coverage over chromosomes and binding profiles to TSS regions, and comparing peak profiles and annotations. It also allows evaluating significant overlap among ChIP-seq datasets. ChIPseeker contains 15,000 bed files from the GEO database, enabling users to compare their data with public datasets to identify co-regulated genes or transcription factor complexes. ChIPseeker provides functions for annotating peaks with nearest genes and genomic regions, including details about exons and introns. It includes visualization tools such as plotAnnoBar, plotAnnoPie, vennpie, and plotDistToTSS. It supports annotation of ChIP-seq data across various species using TxDb objects generated from UCSC, BioMart, or GFF/GTF files. For functional enrichment analysis, it integrates with Bioconductor packages like clusterProfiler, DOSE, and ReactomePA to identify biological themes through Gene Ontology, KEGG, Disease Ontology, and Reactome Pathway. ChIPseeker visualizes peak locations and intensities across the genome and provides tools for comparing peak profiles between experiments. It includes vennplot for calculating and visualizing peak overlaps, and enrichPeakOverlap for statistically rigorous comparisons of ChIP-seq datasets. It also allows testing overlap significance among datasets from different genomes or species. ChIPseeker incorporates GEO datasets, enabling users to compare their data with public datasets to infer co-factors. The package is released under the Artistic-2.0 License and is freely available through Bioconductor. It is supported by the National Natural Science Foundation of China and the Guangdong Natural Science Research Grant.