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  "Type": "Package",
  "Title": "Tools for computational epigenomics",
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  "Date": "2025-07-22",
  "Authors@R": "c(person(\"Mattia\", \"Pelizzola\", role = \"aut\"), person(\"Kamal\", \"Kishore\", role = \"aut\"), person(\"Mattia\", \"Furlan\", email = \"mattia.furlan@iit.it\", role = c(\"ctb\",\"cre\")))",
  "Description": "Tools for computational epigenomics developed for the\nanalysis, integration and simultaneous visualization of various\n(epi)genomics data types across multiple genomic regions in\nmultiple samples.",
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  "Date/Publication": "2026-04-28 12:39:35 UTC",
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  "Maintainer": "Mattia Furlan <mattia.furlan@iit.it>",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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      "page": "compEpiTools-package",
      "title": "Tools for computational epigenomics",
      "topics": [
        "compEpiTools-package",
        "compEpiTools"
      ]
    },
    {
      "page": "countOverlapsInBins-methods",
      "title": "given a query and a subject GRanges returns a matrix of counts of subject in bins of query",
      "topics": [
        "countOverlapsInBins",
        "countOverlapsInBins,GRanges-method",
        "countOverlapsInBins-methods"
      ]
    },
    {
      "page": "distanceFromTSS-methods",
      "title": "Returns the GRanges annotated with info about the closer TSS",
      "topics": [
        "distanceFromTSS",
        "distanceFromTSS,GRanges-method",
        "distanceFromTSS-methods"
      ]
    },
    {
      "page": "enhancers",
      "title": "A GRanges method to define enhancers based on H3K4me1 peaks",
      "topics": [
        "enhancers",
        "enhancers,GRanges-method",
        "enhancers-methods"
      ]
    },
    {
      "page": "findLncRNA",
      "title": "Identify putative long non coding RNAs (lncRNA)",
      "topics": [
        "findLncRNA"
      ]
    },
    {
      "page": "getPromoterClass-methods",
      "title": "Determining the CpG promoter class and the average CpG content",
      "topics": [
        "getPromoterClass",
        "getPromoterClass,TxDb-method",
        "getPromoterClass-methods"
      ]
    },
    {
      "page": "GR2fasta-methods",
      "title": "A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome",
      "topics": [
        "GR2fasta",
        "GR2fasta,GRanges-method",
        "GR2fasta-methods"
      ]
    },
    {
      "page": "GRanges2ucsc-methods",
      "title": "A GRanges method to convert ranges information into UCSC format",
      "topics": [
        "GRanges2ucsc",
        "GRanges2ucsc,GRanges-method",
        "GRanges2ucsc-methods"
      ]
    },
    {
      "page": "GRangesInPromoters-methods",
      "title": "Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters",
      "topics": [
        "GRangesInPromoters",
        "GRangesInPromoters,GRanges-method",
        "GRangesInPromoters-methods"
      ]
    },
    {
      "page": "GRannotate-methods",
      "title": "Based on a GRanges and a TxDb, returns the GRanges with a series of annotations",
      "topics": [
        "GRannotate",
        "GRannotate,GRanges-method",
        "GRannotate-methods"
      ]
    },
    {
      "page": "GRannotateSimple",
      "title": "a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic",
      "topics": [
        "GRannotateSimple",
        "GRannotateSimple,GRanges-method",
        "GRannotateSimple-methods"
      ]
    },
    {
      "page": "GRbaseCoverage-methods",
      "title": "Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range",
      "topics": [
        "GRbaseCoverage",
        "GRbaseCoverage,GRanges-method",
        "GRbaseCoverage-methods"
      ]
    },
    {
      "page": "GRcoverage-methods",
      "title": "based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.",
      "topics": [
        "GRcoverage",
        "GRcoverage,GRanges-method",
        "GRcoverage-methods",
        "GRcoverageInbins",
        "GRcoverageInbins,GRanges-method",
        "GRcoverageInbins-methods"
      ]
    },
    {
      "page": "GRcoverageSummit-methods",
      "title": "Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range",
      "topics": [
        "GRcoverageSummit",
        "GRcoverageSummit,GRanges-method",
        "GRcoverageSummit-methods"
      ]
    },
    {
      "page": "GRenrichment-methods",
      "title": "Determines the enrichment over a set of genomic regions given two BAM files",
      "topics": [
        "GRenrichment",
        "GRenrichment,GRanges-method",
        "GRenrichment-methods"
      ]
    },
    {
      "page": "GRmidpoint-methods",
      "title": "Returns a GRanges containing the mid point of a GRanges",
      "topics": [
        "GRmidpoint",
        "GRmidpoint,GRanges-method",
        "GRmidpoint-methods"
      ]
    },
    {
      "page": "GRsetwidth",
      "title": "Set the width of a GRanges based on the mid point of each region",
      "topics": [
        "GRsetwidth",
        "GRsetwidth,GRanges-method",
        "GRsetwidth-methods"
      ]
    },
    {
      "page": "heatmapData",
      "title": "Based on a list of GRanges, determine various kind of counts before displaying a heatmap",
      "topics": [
        "heatmapData"
      ]
    },
    {
      "page": "heatmapPlot",
      "title": "displays the heatmap based on the data from heatmapData",
      "topics": [
        "heatmapPlot"
      ]
    },
    {
      "page": "makeGtfFromDb",
      "title": "Utilities to transform a TxDb into a GTF file",
      "topics": [
        "featuresLength",
        "featuresLength,TxDb-method",
        "featuresLength-methods",
        "makeGtfFromDb",
        "makeGtfFromDb,TxDb-method",
        "makeGtfFromDb-methods"
      ]
    },
    {
      "page": "matchEnhancers",
      "title": "GRanges method to match enhancers with putative targets sites",
      "topics": [
        "matchEnhancers",
        "matchEnhancers,GRanges-method",
        "matchEnhancers-methods"
      ]
    },
    {
      "page": "overlapOfGRanges-methods",
      "title": "visualization of GRanges overlap",
      "topics": [
        "overlapOfGRanges",
        "overlapOfGRanges,GRanges-method",
        "overlapOfGRanges-methods"
      ]
    },
    {
      "page": "palette2d",
      "title": "build a two dimensional color palette",
      "topics": [
        "palette2d"
      ]
    },
    {
      "page": "plotStallingIndex",
      "title": "Stalling Index plots",
      "topics": [
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      ]
    },
    {
      "page": "simplifyGOterms",
      "title": "simplify a list of GO terms",
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    {
      "page": "stallingIndex",
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      "topics": [
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        "TSS"
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    },
    {
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      "title": "Convert UCSC-formatted genomic positions into a GRanges",
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    {
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      "title": "GRanges method to perform union of peaks keeping the score of the most significant peak",
      "topics": [
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        "unionMaxScore-methods"
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