ChIPseeker: ChIP peak Annotation, Comparison, and Visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

:writing_hand: Authors

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

https://yulab-smu.top

If you use ChIPseeker in published research, please cite:

• Q Wang^#, M Li^#, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, G Yu^*. Exploring epigenomic datasets by ChIPseeker. Current Protocols, 2022, 2(10): e585.
• G Yu^*, LG Wang, QY He^*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383.

Installation

Get the released version from Bioconductor:

## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ChIPseeker")

Or the development version from github:

## install.packages("devtools")
devtools::install_github("YuLab-SMU/ChIPseeker")

Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.