Package: ChIPseeker
Type: Package
Title: ChIPseeker for ChIP peak Annotation, Comparison, and
        Visualization
Version: 1.46.1
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
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-04 14:21:39 UTC
RemoteUrl: https://github.com/bioc/ChIPseeker
RemoteRef: RELEASE_3_22
RemoteSha: c9031f6a319dd648c8b80abedc4c2f6a1e060a91
NeedsCompilation: no
Packaged: 2026-02-21 09:16:25 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>)
Built: R 4.5.2; ; 2026-02-21 09:20:37 UTC; windows
