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.
Package details |
|
---|---|
Author | Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb] |
Bioconductor views | Annotation ChIPSeq MultipleComparison Software Visualization |
Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
License | Artistic-2.0 |
Version | 1.26.2 |
URL | https://guangchuangyu.github.io/software/ChIPseeker |
Package repository | View on Bioconductor |
Installation |
Install the latest version of this package by entering the following in R:
|
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.