README.Rmd

---
output:
  md_document:
    variant: gfm
html_preview: false
---


```{r echo=FALSE, results="hide", message=FALSE}
#library("txtplot")
library("badger")
library("ypages")
library("yulab.utils")
```


# 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/)
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[![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)




```{r comment="", echo=FALSE, results='asis'}
cat(packageDescription('ChIPseeker')$Description)
```


## :writing_hand: Authors

Guangchuang YU 

School of Basic Medical Sciences, Southern Medical University

<https://yulab-smu.top>

If you use `r Biocpkg('ChIPseeker')` in published research, please cite:


+ Q Wang<sup>#</sup>, M Li<sup>#</sup>, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, __G Yu__<sup>\*</sup>. [Exploring epigenomic datasets by ChIPseeker](https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585). __*Current Protocols*__, 2022, 2(10): e585. 
+ __G Yu__<sup>\*</sup>, LG Wang, QY He<sup>\*</sup>. [ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization](http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145). __*Bioinformatics*__. 2015, 31(14):2382-2383. 


## :arrow_double_down: Installation

Get the released version from Bioconductor:

```r
## 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:

```r
## 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](CONDUCT.md).