Exploring Epigenomic Datasets by ChIPseeker

TLDR

Epigenetics shapes phenotype without sequence changes, and the surge of next‑generation sequencing has produced vast epigenomic datasets whose annotation, comparison, visualization, and interpretation are central computational biology tasks. This article explains ChIPseeker’s core functions—data preparation, annotation, comparison, and visualization. ChIPseeker is a freely available open‑source Bioconductor package that offers protocols for preparing epigenomic data, annotating peaks, comparing datasets, visualizing results, performing functional analysis, and generating genome‑wide or locus‑specific distributions, heatmaps, and metaplots, and can be accessed at https://www.bioconductor.org/packages/ChIPseeker. © 2022 Wiley Periodicals LLC.

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. 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. 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. Basic Protocol 6: Genome-wide and locus-specific distribution of epigenomic datasets Basic Protocol 7: Heatmaps and metaplots of epigenomic datasets. Basic Protocol 7: Heatmaps and metaplots of epigenomic datasets.