Package: ChIPseeker
Type: Package
Title: ChIPseeker for ChIP peak Annotation, Comparison, and
        Visualization
Version: 1.49.0
Authors@R: c( 
    person(given = "Guangchuang", family = "Yu",       email = "guangchuangyu@gmail.com",      role  = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")),
    person(given = "Ming",        family = "Li",       email = "limiang929@gmail.com",         role = "ctb"),
    person(given = "Qianwen",     family = "Wang",     email = "treywea@gmail.com",            role = "ctb"),
    person(given = "Yun",         family = "Yan",      email = "youryanyun@gmail.com",         role = "ctb"),
    person(given = "Hervé",       family = "Pagès",    email = "hpages.on.github@gmail.com",   role  = "ctb"),
    person(given = "Michael",     family = "Kluge",    email = "michael.kluge@bio.ifi.lmu.de", role  = "ctb"),
    person(given = "Thomas",      family = "Schwarzl", email = "schwarzl@embl.de",             role  = "ctb"),
    person(given = "Zhougeng",    family = "Xu",       email = "xuzhougeng@163.com",           role  = "ctb"),
	person(given = "Chun-Hui",    family = "Gao",      email="gaospecial@gmail.com",           role  = "ctb", comment=c(ORCID = "0000-0002-1445-7939"))
	)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: 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.
Depends: R (>= 4.1.0)
Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot,
        IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2,
        gplots, graphics, grDevices, gtools, magrittr, methods,
        plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors,
        scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene,
        utils, yulab.utils (>= 0.2.0)
Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram,
        knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown,
        testthat, TxDb.Hsapiens.UCSC.hg38.knownGene
Remotes: GuangchuangYu/enrichplot
URL: https://yulab-smu.top/contribution-knowledge-mining/
BugReports: https://github.com/YuLab-SMU/ChIPseeker/issues
Encoding: UTF-8
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
biocViews: Annotation, ChIPSeq, Software, Visualization,
        MultipleComparison
RoxygenNote: 7.3.3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:06 UTC
RemoteUrl: https://github.com/bioc/ChIPseeker
RemoteRef: HEAD
RemoteSha: f0e31113d0c2879cf2978969077822318c4d84e8
NeedsCompilation: no
Packaged: 2026-05-29 08:42:02 UTC; root
Author: Guangchuang Yu [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>),
  Ming Li [ctb],
  Qianwen Wang [ctb],
  Yun Yan [ctb],
  Hervé Pagès [ctb],
  Michael Kluge [ctb],
  Thomas Schwarzl [ctb],
  Zhougeng Xu [ctb],
  Chun-Hui Gao [ctb] (ORCID: <https://orcid.org/0000-0002-1445-7939>)