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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "epiSeeker" in publications use:'
type: software
license: Artistic-2.0
title: 'epiSeeker: epiSeeker: an R package for Annotation, Comparison and Visualization
  of multi-omics epigenetic data'
version: 1.1.0
doi: 10.1002/cpz1.585
identifiers:
- type: doi
  value: 10.32614/CRAN.package.epiSeeker
abstract: This package implements functions to analyze multi-omics epigenetic data.
  Data of fragment type and base type are supported by epiSeeker. It provides functions
  to retrieve the nearest genes around the peak, annotate genomic region of the peak,
  statistical methods to estimate the significance of overlap among peak data sets,
  and motif analysis. It incorporates the GEO database for users to compare their
  own dataset with those deposited in the 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, overlap of peaks or genes, and the single-base resolution epigenetic
  data by considering the strand, motif, and additional information.
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/epiSeeker
commit: 03bc0c589981d5ed5f1109d7517bca6e1f613bac
url: https://github.com/YuLab-SMU/epiSeeker
date-released: '2026-04-28'
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