{
  "_id": "6a196ed0acfb0bcc41debfc8",
  "Package": "ChIPseeker",
  "Type": "Package",
  "Title": "ChIPseeker for ChIP peak Annotation, Comparison, and\nVisualization",
  "Version": "1.49.0",
  "Authors@R": "c( \nperson(given = \"Guangchuang\", family = \"Yu\",       email = \"guangchuangyu@gmail.com\",      role  = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\")),\nperson(given = \"Ming\",        family = \"Li\",       email = \"limiang929@gmail.com\",         role = \"ctb\"),\nperson(given = \"Qianwen\",     family = \"Wang\",     email = \"treywea@gmail.com\",            role = \"ctb\"),\nperson(given = \"Yun\",         family = \"Yan\",      email = \"youryanyun@gmail.com\",         role = \"ctb\"),\nperson(given = \"Hervé\",       family = \"Pagès\",    email = \"hpages.on.github@gmail.com\",   role  = \"ctb\"),\nperson(given = \"Michael\",     family = \"Kluge\",    email = \"michael.kluge@bio.ifi.lmu.de\", role  = \"ctb\"),\nperson(given = \"Thomas\",      family = \"Schwarzl\", email = \"schwarzl@embl.de\",             role  = \"ctb\"),\nperson(given = \"Zhougeng\",    family = \"Xu\",       email = \"xuzhougeng@163.com\",           role  = \"ctb\"),\nperson(given = \"Chun-Hui\",    family = \"Gao\",      email=\"gaospecial@gmail.com\",           role  = \"ctb\", comment=c(ORCID = \"0000-0002-1445-7939\"))\n)",
  "Maintainer": "Guangchuang Yu <guangchuangyu@gmail.com>",
  "Description": "This package implements functions to retrieve the nearest\ngenes around the peak, annotate genomic region of the peak,\nstatstical methods for estimate the significance of overlap\namong ChIP peak data sets, and incorporate GEO database for\nuser to compare the own dataset with those deposited in\ndatabase. The comparison can be used to infer cooperative\nregulation and thus can be used to generate hypotheses. Several\nvisualization functions are implemented to summarize the\ncoverage of the peak experiment, average profile and heatmap of\npeaks binding to TSS regions, genomic annotation, distance to\nTSS, and overlap of peaks or genes.",
  "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,\nMultipleComparison",
  "RoxygenNote": "7.3.3",
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  "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": {
    "Date": "2026-05-29 08:42:02 UTC",
    "User": "root"
  },
  "Author": "Guangchuang Yu [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6485-8781>),\nMing Li [ctb],\nQianwen Wang [ctb],\nYun Yan [ctb],\nHervé Pagès [ctb],\nMichael Kluge [ctb],\nThomas Schwarzl [ctb],\nZhougeng Xu [ctb],\nChun-Hui Gao [ctb] (ORCID: <https://orcid.org/0000-0002-1445-7939>)",
  "MD5sum": "a829645b5d82e61a8940e2060eda9d77",
  "_user": "bioc",
  "_type": "src",
  "_file": "ChIPseeker_1.49.0.tar.gz",
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  "_created": "2026-05-29T08:42:02.000Z",
  "_published": "2026-05-29T10:47:44.623Z",
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    "login": "guangchuangyu",
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    "description": "Professor of Bioinformatics at Southern Medical University.",
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    "annotatePeak",
    "as.GRanges",
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    "downloadGEObedFiles",
    "downloadGSMbedFiles",
    "dropAnno",
    "enrichAnnoOverlap",
    "enrichPeakOverlap",
    "getAnnoStat",
    "getBioRegion",
    "getGEOgenomeVersion",
    "getGEOInfo",
    "getGEOspecies",
    "getPromoters",
    "getSampleFiles",
    "getTagMatrix",
    "GRangesList",
    "makeBioRegionFromGranges",
    "overlap",
    "peak_Profile_Heatmap",
    "peakHeatmap",
    "peakHeatmap_multiple_Sets",
    "plotAnnoBar",
    "plotAnnoPie",
    "plotAnnoPie.csAnno",
    "plotAvgProf",
    "plotAvgProf2",
    "plotDistToTSS",
    "plotPeakProf",
    "plotPeakProf2",
    "readPeakFile",
    "rel",
    "seq2gene",
    "show",
    "shuffle",
    "tagHeatmap",
    "upsetplot",
    "vennpie",
    "vennplot",
    "vennplot.peakfile"
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      "title": ".",
      "topics": [
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    {
      "page": "dot-ChIPseekerEnv",
      "title": "env function for ChIPseeker",
      "topics": [
        ".ChIPseekerEnv"
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    {
      "page": "annotatePeak",
      "title": "annotatePeak",
      "topics": [
        "annotatePeak"
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    {
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      "title": "as.data.frame.csAnno",
      "topics": [
        "as.data.frame.csAnno"
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      "topics": [
        "as.GRanges"
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    },
    {
      "page": "check_upstream_and_downstream",
      "title": "check upstream and downstream parameter",
      "topics": [
        "check_upstream_and_downstream"
      ]
    },
    {
      "page": "ChIPseekerCache",
      "title": "Name of the ChIPseeker cache environment (internal static variable)",
      "topics": [
        "ChIPseekerCache"
      ]
    },
    {
      "page": "combine_csAnno",
      "title": "combine_csAnno",
      "topics": [
        "combine_csAnno"
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      "page": "covplot",
      "title": "covplot",
      "topics": [
        "covplot"
      ]
    },
    {
      "page": "csAnno-class",
      "title": "Class \"csAnno\" This class represents the output of ChIPseeker Annotation",
      "topics": [
        "csAnno-class",
        "plotAnnoBar,csAnno-method",
        "plotAnnoPie,csAnno-method",
        "plotDistToTSS,csAnno-method",
        "show,csAnno-method",
        "subset,csAnno-method",
        "upsetplot,csAnno-method",
        "vennpie,csAnno-method"
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      "title": "downloadGEObedFiles",
      "topics": [
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    },
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      "title": "downloadGSMbedFiles",
      "topics": [
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    },
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      "page": "dropAnno",
      "title": "dropAnno",
      "topics": [
        "dropAnno"
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      "page": "enrichAnnoOverlap",
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      "title": "enrichPeakOverlap",
      "topics": [
        "enrichPeakOverlap"
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      "page": "getAnnoStat",
      "title": "getAnnoStat",
      "topics": [
        "getAnnoStat"
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    },
    {
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      "title": "getBioRegion",
      "topics": [
        "getBioRegion"
      ]
    },
    {
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      "title": "getGeneAnno",
      "topics": [
        "getGeneAnno"
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    },
    {
      "page": "getGenomicAnnotation",
      "title": "getGenomicAnnotation",
      "topics": [
        "getGenomicAnnotation"
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    },
    {
      "page": "getGEOgenomeVersion",
      "title": "getGEOgenomeVersion",
      "topics": [
        "getGEOgenomeVersion"
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      "page": "getGEOInfo",
      "title": "getGEOInfo",
      "topics": [
        "getGEOInfo"
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      "title": "getGEOspecies",
      "topics": [
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    },
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      "title": "getNearestFeatureIndicesAndDistances",
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        "getNearestFeatureIndicesAndDistances"
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      "page": "getPromoters",
      "title": "getPromoters",
      "topics": [
        "getPromoters"
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      "title": "getSampleFiles",
      "topics": [
        "getSampleFiles"
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      "title": "getTagMatrix",
      "topics": [
        "getTagMatrix"
      ]
    },
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      "topics": [
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      "title": "getTagMatrix2.internal",
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      "page": "info",
      "title": "Information Datasets",
      "topics": [
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        "info",
        "tagMatrixList",
        "ucsc_release"
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    {
      "page": "make_label",
      "title": "make label for figures",
      "topics": [
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    {
      "page": "makeBioRegionFromGranges",
      "title": "makeBioRegionFromGranges",
      "topics": [
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      "source": "ChIPseeker.Rmd",
      "filename": "ChIPseeker.html",
      "title": "ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization",
      "author": "Guangchuang Yu School of Basic Medical Sciences, Southern Medical University",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Citation",
        "Introduction",
        "ChIP profiling",
        "ChIP peaks coverage plot",
        "Profile of ChIP peaks binding to TSS regions",
        "Heatmap of ChIP binding to TSS regions",
        "Average Profile of ChIP peaks binding to TSS region",
        "Profile of ChIP peaks binding to different regions",
        "Binning method for profile of ChIP peaks binding to TSS regions",
        "Profile of ChIP peaks binding to body regions",
        "Profile of ChIP peaks binding to TTS regions",
        "Peak Annotation",
        "Visualize Genomic Annotation",
        "Visualize distribution of TF-binding loci relative to TSS",
        "Functional enrichment analysis",
        "ChIP peak data set comparison",
        "Profile of several ChIP peak data binding to TSS region",
        "Average profiles",
        "Peak heatmaps",
        "Profile of several ChIP peak data binding to body region",
        "ChIP peak annotation comparision",
        "Functional profiles comparison",
        "Overlap of peaks and annotated genes",
        "Statistical testing of ChIP seq overlap",
        "Shuffle genome coordination",
        "Peak overlap enrichment analysis",
        "Data Mining with ChIP seq data deposited in GEO",
        "GEO data collection",
        "Download GEO ChIP data sets",
        "Overlap significant testing",
        "Need helps?",
        "Session Information",
        "References"
      ],
      "created": "2015-05-17 08:47:21",
      "modified": "2024-10-06 03:37:18",
      "commits": 43
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