A guide to utilizing ChIPpeakAnno (Zhu et al. 2010; Zhu 2013) for common analysis of any genmoic interval data such as peak data collected with the classic ChIP-seq or the cutting-edge CUT&RUN experiments, ATAC-seq, and their variants. ChIPpeakAnno offers a range of functions for peak annotaion, visualization, and peak profile comparison.
Several experimental techniques including ChIP-ChIP (Blat and Kleckner 1999), ChIP-seq (Barski et al. 2007; Johnson et al. 2007), and CUT&RUN (Skene and Henikoff 2017) have gained widespread use in molecular biology. These techniques enable the study of protein-DNA interactions by identifying the genomic regions that are associated with specific proteins, such as transcription factor binding sites, or epigenetic markers like histone modification. Through these approaches, researchers gain valuable insights into the regulation of genes and the structure of chromatin.
The analysis involves several key procedures as outlined below, you can also integrate other omics data to gain a more comprehensive view of the gene regulation mechanisms. The steps where ChIPpeakAnno package can be utilized are displayed in pink boxes.