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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "ChIPseeker" in publications use:'
type: software
license: Artistic-2.0
title: 'ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization'
version: 1.41.3
doi: 10.1002/cpz1.585
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ChIPseeker
abstract: 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:
- family-names: Yu
  given-names: Guangchuang
  email: guangchuangyu@gmail.com
  orcid: https://orcid.org/0000-0002-6485-8781
preferred-citation:
  type: article
  title: Exploring epigenomic datasets by ChIPseeker
  authors:
  - family-names: Wang
    given-names: Qianwen
  - family-names: Li
    given-names: Ming
  - family-names: Wu
    given-names: Tianzhi
  - family-names: Zhan
    given-names: Li
  - family-names: Li
    given-names: Lin
  - family-names: Chen
    given-names: Meijun
  - family-names: Xie
    given-names: Wenqin
  - family-names: Xie
    given-names: Zijing
  - family-names: Hu
    given-names: Erqiang
  - family-names: Xu
    given-names: Shuangbin
  - family-names: Yu
    given-names: Guangchuang
    email: guangchuangyu@gmail.com
    orcid: https://orcid.org/0000-0002-6485-8781
  journal: Current Protocols
  year: '2022'
  volume: '2'
  issue: '10'
  doi: 10.1002/cpz1.585
  url: https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
  start: e585
repository: https://bioc.r-universe.dev
repository-code: https://github.com/YuLab-SMU/ChIPseeker
commit: 02858e4d3105deafe7132c35c0ba9d70e0dfad38
url: https://yulab-smu.top/contribution-knowledge-mining/
contact:
- family-names: Yu
  given-names: Guangchuang
  email: guangchuangyu@gmail.com
  orcid: https://orcid.org/0000-0002-6485-8781
references:
- type: article
  title: 'ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison
    and visualization'
  authors:
  - family-names: Yu
    given-names: Guangchuang
  - family-names: Wang
    given-names: Li-Gen
  - family-names: He
    given-names: Qing-Yu
  journal: Bioinformatics
  year: '2015'
  volume: '31'
  issue: '14'
  doi: 10.1093/bioinformatics/btv145
  start: 2382-2383