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.
Keywords: ChIPseeker; annotation; comparison; epigenetic; visualization.
© 2022 Wiley Periodicals LLC.