{
  "_id": "6a1ae00d1d7bb097a09ec93c",
  "Package": "chipenrich",
  "Type": "Package",
  "Title": "Gene Set Enrichment For ChIP-seq Peak Data",
  "Version": "2.37.0",
  "Date": "2025-07-22",
  "Authors@R": "c(\nperson(c(\"Ryan\",\"P.\"),\"Welch\",role = c(\"aut\",\"cph\"),email = \"welchr@umich.edu\"),\nperson(\"Chee\",\"Lee\",role = c(\"aut\"),email = \"cheelee@umich.edu\"),\nperson(c(\"Raymond\",\"G.\"),\"Cavalcante\",role = c(\"aut\"),email = \"rcavalca@umich.edu\"),\nperson(\"Kai\",\"Wang\",role = c(\"cre\"),email = \"wangdaha@umich.edu\"),\nperson(\"Chris\",\"Lee\",role = c(\"aut\"),email = \"leetaiyi@umich.edu\"),\nperson(c(\"Laura\",\"J.\"),\"Scott\",role = c(\"ths\"), email = \"ljst@umich.edu\"),\nperson(c(\"Maureen\",\"A.\"),\"Sartor\",role = c(\"ths\"),email = \"sartorma@med.umich.edu\"))",
  "Description": "ChIP-Enrich and Poly-Enrich perform gene set enrichment\ntesting using peaks called from a ChIP-seq experiment. The\nmethod empirically corrects for confounding factors such as the\nlength of genes, and the mappability of the sequence\nsurrounding genes.",
  "biocViews": "ImmunoOncology, ChIPSeq, Epigenetics, FunctionalGenomics,\nGeneSetEnrichment, HistoneModification, Regression",
  "License": "GPL-3",
  "LazyLoad": "yes",
  "Maintainer": "Kai Wang <wangdaha@umich.edu>",
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  "Collate": "'assign_peaks.R' 'test_broadenrich.R' 'peaks_per_gene.R'\n'read.R' 'randomize.R' 'setup.R' 'supported.R' 'utils.R'\n'constants.R' 'plot_gene_coverage.R' 'broadenrich.R'\n'test_chipapprox.R' 'test_chipenrich.R'\n'test_chipenrich_slow.R' 'test_fisher.R' 'test_binomial.R'\n'test_approx.R' 'plot_chipenrich_spline.R' 'plot_dist_to_tss.R'\n'chipenrich.R' 'chipenrich_package_doc.R' 'test_polyapprox.R'\n'test_polyenrich_weighted.R' 'test_polyenrich_slow.R'\n'test_polyenrich.R' 'plot_polyenrich_spline.R' 'polyenrich.R'\n'hybrid.R' 'peak_weights.R' 'peaks2genes.R' 'test_proxReg.R'\n'proxReg.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:07 UTC",
  "RemoteUrl": "https://github.com/bioc/chipenrich",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:17:19 UTC",
    "User": "root"
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  "Author": "Ryan P. Welch [aut, cph],\nChee Lee [aut],\nRaymond G. Cavalcante [aut],\nKai Wang [cre],\nChris Lee [aut],\nLaura J. Scott [ths],\nMaureen A. Sartor [ths]",
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  "_created": "2026-05-30T09:17:19.000Z",
  "_published": "2026-05-30T13:03:09.610Z",
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    "chipseq",
    "epigenetics",
    "functionalgenomics",
    "genesetenrichment",
    "histonemodification",
    "regression"
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    "assign_peaks",
    "broadenrich",
    "calc_peak_gene_overlap",
    "chipenrich",
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    "load_peaks",
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    "supported_locusdefs",
    "supported_methods",
    "supported_read_lengths"
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    {
      "page": "assign_peak_segments",
      "title": "Assign whole peaks to all overlapping defined gene loci.",
      "topics": [
        "assign_peak_segments"
      ]
    },
    {
      "page": "assign_peaks",
      "title": "Assign peak midpoints to defined gene loci.",
      "topics": [
        "assign_peaks"
      ]
    },
    {
      "page": "broadenrich",
      "title": "Run Broad-Enrich on broad genomic regions",
      "concept": [
        "enrichment functions"
      ],
      "topics": [
        "broadenrich"
      ]
    },
    {
      "page": "calc_peak_gene_overlap",
      "title": "Add peak overlap and ratio to result of 'num_peaks_per_gene()'",
      "topics": [
        "calc_peak_gene_overlap"
      ]
    },
    {
      "page": "chipenrich",
      "title": "Run ChIP-Enrich on narrow genomic regions",
      "concept": [
        "enrichment functions"
      ],
      "topics": [
        "chipenrich"
      ]
    },
    {
      "page": "chipenrich_package",
      "title": "chipenrich: Gene Set Enrichment For ChIP-seq Peak Data and Other Genomic Regions",
      "topics": [
        "chipenrich_package"
      ]
    },
    {
      "page": "filter_genesets",
      "title": "Function to filter genesets by locus definition and size",
      "topics": [
        "filter_genesets"
      ]
    },
    {
      "page": "genome_to_organism",
      "title": "Get the correct organism code based on genome",
      "topics": [
        "genome_to_organism"
      ]
    },
    {
      "page": "genome_to_orgdb",
      "title": "Get Entrez ID to gene symbol mappings for custom locus definitions",
      "topics": [
        "genome_to_orgdb"
      ]
    },
    {
      "page": "get_test_method",
      "title": "Get the test function name from the method name",
      "topics": [
        "get_test_method"
      ]
    },
    {
      "page": "hybridenrich",
      "title": "Running Hybrid test, either from scratch or using two results files",
      "topics": [
        "hybridenrich"
      ]
    },
    {
      "page": "load_peaks",
      "title": "Convert a BEDX+Y data.frame and into GRanges",
      "topics": [
        "load_peaks"
      ]
    },
    {
      "page": "num_peaks_per_gene",
      "title": "Aggregate peak assignments over the 'gene_id' column",
      "topics": [
        "num_peaks_per_gene"
      ]
    },
    {
      "page": "peaks2genes",
      "title": "Run the test process up to, but not including the enrichment tests.",
      "topics": [
        "peaks2genes"
      ]
    },
    {
      "page": "plot_chipenrich_spline",
      "title": "QC plot for ChIP-Enrich",
      "topics": [
        "plot_chipenrich_spline"
      ]
    },
    {
      "page": "plot_dist_to_tss",
      "title": "Plot histogram of distance from peak to nearest TSS",
      "topics": [
        "plot_dist_to_tss"
      ]
    },
    {
      "page": "plot_gene_coverage",
      "title": "QC plot for Broad-Enrich",
      "topics": [
        "plot_gene_coverage"
      ]
    },
    {
      "page": "plot_polyenrich_spline",
      "title": "QC plot for Poly-Enrich",
      "topics": [
        "plot_polyenrich_spline"
      ]
    },
    {
      "page": "polyenrich",
      "title": "Run Poly-Enrich on narrow genomic regions",
      "concept": [
        "enrichment functions"
      ],
      "topics": [
        "polyenrich"
      ]
    },
    {
      "page": "post_process_enrichments",
      "title": "Post process the 'data.frame' of enrichment results",
      "topics": [
        "post_process_enrichments"
      ]
    },
    {
      "page": "postprocess_peak_grs",
      "title": "A helper function to post-process peak GRanges",
      "topics": [
        "postprocess_peak_grs"
      ]
    },
    {
      "page": "proxReg",
      "title": "Run Proximity Regulation test on a set of narrow genomic regions",
      "topics": [
        "proxReg"
      ]
    },
    {
      "page": "read_bed",
      "title": "Read files containing peaks or genomic regions",
      "topics": [
        "read_bed"
      ]
    },
    {
      "page": "read_geneset",
      "title": "Function to read custom gene sets from file",
      "topics": [
        "read_geneset"
      ]
    },
    {
      "page": "read_ldef",
      "title": "Function to read custom locus definition from file",
      "topics": [
        "read_ldef"
      ]
    },
    {
      "page": "read_mappa",
      "title": "Function to read custom mappability files",
      "topics": [
        "read_mappa"
      ]
    },
    {
      "page": "recode_peaks",
      "title": "Recode a vector of number of peaks to binary based on threshold",
      "topics": [
        "recode_peaks"
      ]
    },
    {
      "page": "reset_ncores_for_windows",
      "title": "Reset n_cores for Windows",
      "topics": [
        "reset_ncores_for_windows"
      ]
    },
    {
      "page": "setup_genesets",
      "title": "Function to setup genesets",
      "topics": [
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    {
      "page": "setup_locusdef",
      "title": "Function to setup locus definitions",
      "topics": [
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      "title": "Function to setup mappability",
      "topics": [
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    {
      "page": "supported_genesets",
      "title": "Display supported genesets for gene set enrichment.",
      "topics": [
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    },
    {
      "page": "supported_genomes",
      "title": "Display supported genomes.",
      "topics": [
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    },
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      "title": "Display supported locus definitions",
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    },
    {
      "page": "supported_methods",
      "title": "Display supported gene set enrichment methods.",
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    {
      "page": "supported_read_lengths",
      "title": "Display supported read lengths for mappability",
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  "_vignettes": [
    {
      "source": "chipenrich-vignette.Rmd",
      "filename": "chipenrich-vignette.html",
      "title": "chipenrich: Gene Set Enrichment For ChIP-seq Peak Data",
      "author": "Ryan P. Welch, Chee Lee, Raymond G. Cavalcante, Chris Lee, Kai Wang, Laura J. Scott, Maureen A. Sartor",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Concepts and Usage",
        "Peaks",
        "Genomes",
        "Locus Definitions",
        "Built-in locus definitions",
        "Custom locus definitions",
        "Selecting a locus definition",
        "Gene Sets",
        "Built-in gene sets",
        "Custom gene sets",
        "Mappability",
        "Built-in mappability",
        "Custom mappability",
        "Testing for enrichment",
        "broadenrich()",
        "chipenrich()",
        "polyenrich()",
        "hybridenrich()",
        "proxReg()",
        "QC Plots",
        "Peak distance to TSS distribution",
        "Presence of peak versus locus length",
        "Number of peaks versus locus length",
        "Gene coverage versus locus length",
        "Output",
        "Assigned peaks",
        "Peaks-per-gene",
        "Gene set enrichment results",
        "Assessing Type I Error with Randomizations",
        "References"
      ],
      "created": "2016-08-26 15:18:54",
      "modified": "2021-06-03 19:46:52",
      "commits": 39
    }
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