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README.Rmd
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README.Rmd
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---
output:
md_document:
variant: markdown_github
html_preview: false
---
```{r echo=FALSE, results="hide", message=FALSE}
#library("txtplot")
library("badger")
library("ypages")
```
# ChIPseeker: ChIP peak Annotation, Comparison, and Visualization
<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ChIPseeker/ChIPseeker.png" height="200" align="right" />
`r badge_bioc_release("ChIPseeker", "green")`
`r badge_devel("guangchuangyu/ChIPseeker", "green")`
[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ChIPseeker.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ChIPseeker.html#since)
[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![codecov](https://codecov.io/gh/GuangchuangYu/ChIPseeker/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ChIPseeker/)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ChIPseeker/commits/master)
[![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ChIPseeker.svg)](https://github.com/GuangchuangYu/ChIPseeker/network)
[![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ChIPseeker.svg)](https://github.com/GuangchuangYu/ChIPseeker/stargazers)
[![platform](http://www.bioconductor.org/shields/availability/devel/ChIPseeker.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ChIPseeker.html#archives)
[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ChIPseeker.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ChIPseeker/)
[![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ChIPseeker/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ChIPseeker)
[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ChIPseeker/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ChIPseeker)
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 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.
For details, please visit our project website, <https://guangchuangyu.github.io/software/ChIPseeker>.
+ [Documentation](https://guangchuangyu.github.io/software/ChIPseeker/documentation/)
+ [Featured Articles](https://guangchuangyu.github.io/software/ChIPseeker/featuredArticles/)
+ [Feedback](https://guangchuangyu.github.io/software/ChIPseeker/#feedback)
[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ChIPseeker&url=http://bioinformatics.oxfordjournals.org/content/31/14/2382&screen_name=guangchuangyu)
`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`
`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`
------------------------------------------------------------------------
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.
`r badge_doi("10.1093/bioinformatics/btv145", "green")`
`r badge_altmetric("3781087", "green")`
------------------------------------------------------------------------
### Citation
<img src="https://guangchuangyu.github.io/software/ChIPseeker/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
### Download stats
`r badge_download_bioc("ChIPseeker")`
`r badge_bioc_download("ChIPseeker", "total", "blue")`
`r badge_bioc_download("ChIPseeker", "month", "blue")`
<img src="https://guangchuangyu.github.io/software/ChIPseeker/index_files/figure-html/dlstats-1.png" width="890"/>
## Contributing
We welcome any contributions! By participating in this project you agree to
abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).