{
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  "Package": "extraChIPs",
  "Version": "1.17.4",
  "Title": "Additional functions for working with ChIP-Seq data",
  "Authors@R": "person(\"Stevie\", \"Pederson\", \nemail = \"stephen.pederson.au@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8197-3303\")\n)",
  "Description": "This package builds on existing tools and adds some simple\nbut extremely useful capabilities for working wth ChIP-Seq\ndata. The focus is on detecting differential binding\nwindows/regions. One set of functions focusses on\nset-operations retaining mcols for GRanges objects, whilst\nanother group of functions are to aid visualisation of results.\nCoercion to tibble objects is also implemented.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/smped/extraChIPs",
  "BugReports": "https://github.com/smped/extraChIPs/issues",
  "biocViews": "ChIPSeq, HiC, Sequencing, Coverage",
  "BiocType": "Software",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
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  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-28 17:26:49 UTC",
  "RemoteUrl": "https://github.com/bioc/extraChIPs",
  "RemoteRef": "HEAD",
  "RemoteSha": "6379747bab4619c0862d5305f9077fbeebeee01c",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-29 07:29:11 UTC",
    "User": "root"
  },
  "Author": "Stevie Pederson [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8197-3303>)",
  "Maintainer": "Stevie Pederson <stephen.pederson.au@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "extraChIPs_1.17.4.tar.gz",
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  "_expires": "2026-10-12T18:36:55.000Z",
  "_created": "2026-06-29T07:29:11.000Z",
  "_published": "2026-07-04T18:36:57.745Z",
  "_bioccheck": {
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    "warning": 1,
    "note": 8
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28355512373",
  "_status": "success",
  "_upstream": "https://github.com/bioc/extraChIPs",
  "_commit": {
    "id": "6379747bab4619c0862d5305f9077fbeebeee01c",
    "author": "Stevie Ped <stephen.pederson.au@gmail.com>",
    "committer": "Stevie Ped <stephen.pederson.au@gmail.com>",
    "message": "Version bump after bugfix\n",
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  "_assets": [
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    "extra/citation.json",
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    "extra/contents.json",
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    "manual.pdf"
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  "_homeurl": "https://github.com/smped/extrachips",
  "_realowner": "bioc",
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  "_exports": [
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    "bestOverlap",
    "centrePeaks",
    "chopMC",
    "collapseGenes",
    "colToRanges",
    "defineRegions",
    "defineSeqinfo",
    "distinctMC",
    "dualFilter",
    "fitAssayDiff",
    "getProfileData",
    "grlToSE",
    "importPeaks",
    "intersectMC",
    "makeConsensus",
    "mapByFeature",
    "mapGrlCols",
    "mergeByCol",
    "mergeByHMP",
    "mergeBySig",
    "partitionRanges",
    "plotAssayDensities",
    "plotAssayHeatmap",
    "plotAssayPCA",
    "plotAssayRle",
    "plotGrlCol",
    "plotHFGC",
    "plotOverlaps",
    "plotPairwise",
    "plotPie",
    "plotProfileHeatmap",
    "plotSplitDonut",
    "propOverlap",
    "reduceMC",
    "setdiffMC",
    "stitchRanges",
    "unionMC",
    "voomWeightsFromCPM"
  ],
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      "title": "Datasets for an example region",
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        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_hic",
      "title": "Datasets for an example region",
      "object": "ex_hic",
      "file": "ex_hic.rda",
      "class": [
        "GInteractions"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_prom",
      "title": "Datasets for an example region",
      "object": "ex_prom",
      "file": "ex_prom.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_trans",
      "title": "Datasets for an example region",
      "object": "ex_trans",
      "file": "ex_trans.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "grch37.cytobands",
      "title": "Cytogenetic bands",
      "object": "grch37.cytobands",
      "file": "grch37.cytobands.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd",
        "name",
        "gieStain"
      ],
      "rows": 862,
      "table": true,
      "tojson": true
    },
    {
      "name": "grch38.cytobands",
      "title": "Cytogenetic bands",
      "object": "grch38.cytobands",
      "file": "grch38.cytobands.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd",
        "name",
        "gieStain"
      ],
      "rows": 862,
      "table": true,
      "tojson": true
    },
    {
      "name": "peaks",
      "title": "Datasets for the Fixed-Width Vignette",
      "object": "peaks",
      "file": "peaks.rda",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "se",
      "title": "Datasets for the Fixed-Width Vignette",
      "object": "se",
      "file": "se.rda",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "addDiffStatus-methods",
      "title": "Add a status column",
      "topics": [
        "addDiffStatus",
        "addDiffStatus,data.frame-method",
        "addDiffStatus,DataFrame-method",
        "addDiffStatus,GRanges-method",
        "addDiffStatus,GRangesList-method",
        "addDiffStatus,SummarizedExperiment-method"
      ]
    },
    {
      "page": "as_tibble",
      "title": "Convert to a tibble",
      "topics": [
        "as_tibble",
        "as_tibble.DataFrame",
        "as_tibble.GenomicRanges",
        "as_tibble.GInteractions",
        "as_tibble.Seqinfo",
        "as_tibble.SummarizedExperiment",
        "as_tibble.TopTags"
      ]
    },
    {
      "page": "bestOverlap-methods",
      "title": "Find the best overlap between GRanges",
      "topics": [
        "bestOverlap",
        "bestOverlap,GRanges,GRanges-method",
        "bestOverlap,GRanges,GRangesList-method"
      ]
    },
    {
      "page": "centrePeaks-methods",
      "title": "Re-estimate peak centres from coverage",
      "topics": [
        "centrePeaks",
        "centrePeaks,GRanges,BamFile-method",
        "centrePeaks,GRanges,BamFileList-method",
        "centrePeaks,GRanges,BigWigFile-method",
        "centrePeaks,GRanges,BigWigFileList-method",
        "centrePeaks,GRanges,character-method"
      ]
    },
    {
      "page": "chopMC",
      "title": "Keep unique ranges and collapse mcols",
      "topics": [
        "chopMC"
      ]
    },
    {
      "page": "collapseGenes",
      "title": "Collapse a vector of gene names",
      "topics": [
        "collapseGenes"
      ]
    },
    {
      "page": "colToRanges-methods",
      "title": "Coerce a column to a GRanges object",
      "topics": [
        "colToRanges",
        "colToRanges,data.frame-method",
        "colToRanges,DataFrame-method",
        "colToRanges,GRanges-method"
      ]
    },
    {
      "page": "cytobands",
      "title": "Cytogenetic bands",
      "topics": [
        "cytobands",
        "grch37.cytobands",
        "grch38.cytobands"
      ]
    },
    {
      "page": "defineRegions",
      "title": "Define Genomic Regions Based on Gene Annotations",
      "topics": [
        "defineRegions"
      ]
    },
    {
      "page": "defineSeqinfo",
      "title": "Use package data to define a Seqinfo object",
      "topics": [
        "defineSeqinfo"
      ]
    },
    {
      "page": "distinctMC",
      "title": "Keep distinct ranges and mcols",
      "topics": [
        "distinctMC"
      ]
    },
    {
      "page": "dualFilter",
      "title": "Apply two filters to sliding windows",
      "topics": [
        "dualFilter"
      ]
    },
    {
      "page": "ex_datasets",
      "title": "Datasets for an example region",
      "topics": [
        "ex_datasets",
        "ex_genes",
        "ex_hic",
        "ex_prom",
        "ex_trans"
      ]
    },
    {
      "page": "fitAssayDiff-methods",
      "title": "Detect Differential ChIP Signal",
      "topics": [
        "fitAssayDiff",
        "fitAssayDiff,SummarizedExperiment-method"
      ]
    },
    {
      "page": "fixed_width_datasets",
      "title": "Datasets for the Fixed-Width Vignette",
      "topics": [
        "fixed_width_datasets",
        "peaks",
        "se"
      ]
    },
    {
      "page": "getProfileData-methods",
      "title": "Get Profile Data surrounding specified ranges",
      "topics": [
        "getProfileData",
        "getProfileData,BigWigFile,GenomicRanges-method",
        "getProfileData,BigWigFileList,GenomicRanges-method",
        "getProfileData,character,GenomicRanges-method"
      ]
    },
    {
      "page": "grlToSE-methods",
      "title": "Set columns from a GRangesList as Assays in a SummarizedExperiment",
      "topics": [
        "grlToSE",
        "grlToSE,GRangesList-method"
      ]
    },
    {
      "page": "importPeaks",
      "title": "Import peaks",
      "topics": [
        "importPeaks"
      ]
    },
    {
      "page": "makeConsensus",
      "title": "Make a set of consensus peaks",
      "topics": [
        "makeConsensus"
      ]
    },
    {
      "page": "mapByFeature",
      "title": "Map Genomic Ranges to genes using defined features",
      "topics": [
        "mapByFeature"
      ]
    },
    {
      "page": "mapGrlCols",
      "title": "Collapse a GRangesList adding multiple columns from each element",
      "topics": [
        "mapGrlCols"
      ]
    },
    {
      "page": "mergeByCol-methods",
      "title": "Merge sliding windows using a specified column",
      "topics": [
        "mergeByCol",
        "mergeByCol,GenomicRanges-method",
        "mergeByCol,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "mergeByHMP-methods",
      "title": "Merge Sliding Windows using the Harmonic Mean P",
      "topics": [
        "mergeByHMP",
        "mergeByHMP,GenomicRanges-method",
        "mergeByHMP,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "mergeBySig-methods",
      "title": "Merge overlapping ranges based on p-values",
      "topics": [
        "mergeBySig",
        "mergeBySig,GenomicRanges-method",
        "mergeBySig,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "partitionRanges-methods",
      "title": "Partition a set of Genomic Ranges",
      "topics": [
        "partitionRanges",
        "partitionRanges,GRanges,GRanges-method"
      ]
    },
    {
      "page": "plotAssayDensities-methods",
      "title": "Plot Densities for any assay within a SummarizedExperiment",
      "topics": [
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