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  "Title": "Characterization of Methylation using positional ENTanglement",
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  "Description": "CMEnt implements a correlation-based method for\nidentifying Differentially Methylated Regions (DMRs) from\ngenomic seeds, commonly Differentially Methylated Positions\n(DMPs). The package expands regions around significant seeds\nconsidering both statistical significance and biological\nrelevance of methylation changes. It supports array-based\n(450K, EPIC, EPICv2) and NGS methylation data through\ntabix-indexed files, provides DMR interaction analysis via\nmotif similarity, and includes comprehensive visualization\ntools including circos plots and beta value heatmaps.",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-06-12 11:14:49 UTC",
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  "Author": "Vasileios Lemonidis [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-6446-3536>),\nCenter for Oncological Research, University of Antwerp [cph, fnd],\nStichting Tegen Kanker [fnd]",
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      "title": "Annotate DMRs with Gene Information",
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      "title": "Augment BSseq Object",
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      ]
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    {
      "page": "buildDMRs",
      "title": "Build Differentially Methylated Regions (DMRs) from Differentially Methylated Positions (seeds)",
      "topics": [
        "buildDMRs"
      ]
    },
    {
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      "title": "Combine spatially correlated p-values with comb-p style SLK correction",
      "topics": [
        "combinePvalues"
      ]
    },
    {
      "page": "computeDMRsInteraction",
      "title": "Compute Motif-Based DMR Interactions",
      "topics": [
        "computeDMRsInteraction"
      ]
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    {
      "page": "convertBetaToTabix",
      "title": "Convert Beta File to Tabix-Indexed Format",
      "topics": [
        "convertBetaToTabix"
      ]
    },
    {
      "page": "extractDMRMotifs",
      "title": "Extract DMR Motif Frequencies",
      "topics": [
        "extractDMRMotifs"
      ]
    },
    {
      "page": "findDMPsArray",
      "title": "Find DMPs from methylation array beta values using limma",
      "topics": [
        "findDMPsArray"
      ]
    },
    {
      "page": "findDMPsBSSeq",
      "title": "Find DMPs using DSS on BSseq objects",
      "topics": [
        "findDMPsBSSeq"
      ]
    },
    {
      "page": "getBetaHandler",
      "title": "Create a BetaHandler object for efficient beta value access",
      "topics": [
        "getBetaHandler"
      ]
    },
    {
      "page": "getDMRSequences",
      "title": "Extract DNA Sequences for DMRs",
      "topics": [
        "getDMRSequences"
      ]
    },
    {
      "page": "getSortedGenomicLocs",
      "title": "Get Sorted Array Locations",
      "topics": [
        "getSortedGenomicLocs"
      ]
    },
    {
      "page": "launchCMEntViewer",
      "title": "Launch CMEnt Interactive Viewer",
      "topics": [
        "launchCMEntViewer"
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      "title": "Load CMEnt Example Resources",
      "topics": [
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        "loadExampleInputDataChr21And22",
        "loadExampleInputDataChr5And11"
      ]
    },
    {
      "page": "orderByLoc",
      "title": "Orders a vector of indices according to their corresponding genomic locations (chromosome and position). This function is useful for sorting site sites or other genomic features by their physical positions.",
      "topics": [
        "orderByLoc"
      ]
    },
    {
      "page": "plotAutoDMRsCircos",
      "title": "Plot DMR Circos Views Using Automatically Selected Regions",
      "topics": [
        "plotAutoDMRsCircos"
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      "title": "Plot DMR",
      "topics": [
        "plotDMR"
      ]
    },
    {
      "page": "plotDMRBlockFormation",
      "title": "Plot Intermediate DMR Block Formation Diagnostics",
      "topics": [
        "plotDMRBlockFormation"
      ]
    },
    {
      "page": "plotDMRs",
      "title": "Plot Multiple DMRs in a Grid",
      "topics": [
        "plotDMRs"
      ]
    },
    {
      "page": "plotDMRsCircos",
      "title": "Plot Circos Visualization of DMRs",
      "topics": [
        "plotDMRsCircos"
      ]
    },
    {
      "page": "plotDMRsManhattan",
      "title": "Plot Manhattan-Style View of DMR Scores",
      "topics": [
        "plotDMRsManhattan"
      ]
    },
    {
      "page": "readCustomMethylationBedData",
      "title": "Read and Process Custom Methylation BED Data",
      "topics": [
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    },
    {
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      "title": "Add Complementary Classification Scores to DMRs",
      "topics": [
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      ]
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    {
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      "title": "Simulate DMRs while preserving local methylation structure",
      "topics": [
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      ]
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      "title": "Sort Beta File by Genomic Coordinates",
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