Exploring Epigenomic Datasets by ChIPseeker

Abstract In many aspects of life, epigenetics, or the altering of phenotype without changes in sequences, play an essential role in biological function. A vast number of epigenomic datasets are emerging as a result of the advent of next‐generation sequencing. Annotation, comparison, visualization, and interpretation of epigenomic datasets remain key aspects of computational biology. ChIPseeker is a Bioconductor package for performing these analyses among variable epigenomic datasets. The fundamental functions of ChIPseeker, including data preparation, annotation, comparison, and visualization, are explained in this article. ChIPseeker is a freely available open‐source package that may be found at https://www.bioconductor.org/packages/ChIPseeker . © 2022 Wiley Periodicals LLC. Basic Protocol 1 : ChIPseeker and epigenomic dataset preparation Basic Protocol 2 : Annotation of epigenomic datasets Basic Protocol 3 : Comparison of epigenomic datasets Basic Protocol 4 : Visualization of annotated results Basic Protocol 5 : Functional analysis of epigenomic datasets Basic Protocol 6 : Genome‐wide and locus‐specific distribution of epigenomic datasets Basic Protocol 7 : Heatmaps and metaplots of epigenomic datasets