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.

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://ygc.name

Citation

Please cite the following article when using ChIPseeker:

Yu G, Wang LG and He QY.
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Bioinformatics, 2015, 31(14):2382-2383.
doi: 10.1093/bioinformatics/btv145

URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145

License

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

Installation

To install:

• the latest released version: biocLite("ChIPseeker")
• the latest development version: install_github("GuangchuangYu/ChIPseeker")

Documentation

• Bug of R package ChIPpeakAnno
• parsing BED coordinates
• Peak Annotation
• Multiple Annotation
• Visualization Methods
• upsetplot
• functional enrichment analysis with NGS data
• ChIPseq data mining with ChIPseeker

Find out more at http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html and check out the vignette.

To view the vignette of ChIPseeker installed in your system, start R and enter:

vignette("ChIPseeker", "ChIPseeker")

Bugs/Feature requests

• If you have any, let me know. Thx!