Tool: ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare their 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.

Homepage: https://guangchuangyu.github.io/ChIPseeker/

Documentation: https://guangchuangyu.github.io/ChIPseeker/documentation/

Issue/Question: https://guangchuangyu.github.io/ChIPseeker/#feedback

Citation

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

Example

http://f1000research.com/articles/5-1542/v1

chip-seq r visualization bioconductor chipseeker

• 3,645 views • link

updated 3.1 years ago by Ram

• written 10.1 years ago by Guangchuang Yu

1 answer

Hi Guang,

I am fairly new to coding and am trying to work through the ChIPSeeker package using my own data in R. I have gotten to section 7 to do the ChIP peak data comparison but I am not sure how to input multiple files (.bed) into the getTagMatrix command. I also tried to create a list with the files to run in, but it didn't work. I want to generate this: "Average Profiles of ChIP peaks among different experiments" plot using my own data.

Can you give me advice?

Thanks Swadha

• 0 views • link

written 10.0 years ago by s.singh •