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  "Package": "dnaEPICO",
  "Title": "dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array\nData",
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  "Date": "2026-01-18",
  "Authors@R": "c(person(\"Paul\", \"Ruiz\", role = c(\"aut\", \"cre\"),\nemail = \"ruizpint@qut.edu.au\", comment = c(ORCID = \"0009-0007-6714-3566\")),\nperson(\"Divya\", \"Mehta\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7971-7255\")))",
  "Description": "A modular and reproducible workflow for preprocessing and\nanalysing Illumina DNA methylation array data from the EPICv2,\nEPIC, and 450K platforms. The package integrates quality\ncontrol, probe filtering, cell-type deconvolution, phenotype\npreparation, generalised linear models, linear mixed-effects\nmodels, and automated report generation. It builds on\nestablished Bioconductor infrastructure and wraps commonly used\ntools including 'minfi', 'ENmix', and 'wateRmelon', with\nsupport for both local execution and high-performance computing\nworkflows.",
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  "Date/Publication": "2026-05-28 19:50:14 UTC",
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    "estimateLCMinfiEwasWater",
    "estimateSvaEnmixControls",
    "extractMake",
    "extractMetricsMinfiEwasWater",
    "filterProbesMinfiEwasWater",
    "filterSamplesMinfiEwasWater",
    "fitMethylationGLM_T1Models",
    "fitMethylationGLMM_T1T2Models",
    "loadMetricsPreprocessingPheno",
    "mergeSvaTargetsEnmix",
    "methylationGLM_T1",
    "methylationGLMM_T1T2",
    "normalizeMinfiEwasWater",
    "plotAssessmentMinfiEwasWater",
    "plotCtrlMinfiEwasWater",
    "plotMethylationGLM_T1Diagnostics",
    "plotMethylationGLM_T1Distributions",
    "plotMethylationGLMM_T1T2Diagnostics",
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    "plotNormalizationMinfiEwasWater",
    "plotRawDensityMinfiEwasWater",
    "plotSexMinfiEwasWater",
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    "predictSexMinfiEwasWater",
    "prepareDnamReportInputs",
    "prepareMethylationGLM_T1Data",
    "prepareMethylationGLMM_T1T2Data",
    "preprocessingMinfiEwasWater",
    "preprocessingPheno",
    "readPhenotypeTargets",
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    "renderDnamReport",
    "splitTimepointsPreprocessingPheno",
    "summarizeMethylationGLM_T1Models",
    "summarizeMethylationGLMM_T1T2Models",
    "summarizeTimepointsMethylationGLMM_T1T2",
    "svaEnmix",
    "writeMethylationGLM_T1Outputs",
    "writeMethylationGLMM_T1T2Outputs",
    "writePhenoLCMinfiEwasWater",
    "writePreprocessingPhenoOutputs",
    "writeSvaEnmixOutputs"
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      "page": "analyzeSvaEnmix",
      "title": "Analyze surrogate variables against Sentrix chip and position factors",
      "topics": [
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    },
    {
      "page": "annotateMethylationGLM_T1Summaries",
      "title": "Annotate one-timepoint GLM summary tables with array annotation metadata",
      "topics": [
        "annotateMethylationGLM_T1Summaries"
      ]
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    {
      "page": "annotateMethylationGLMM_T1T2Summaries",
      "title": "Annotate longitudinal mixed-effects summary tables with array annotation metadata",
      "topics": [
        "annotateMethylationGLMM_T1T2Summaries"
      ]
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    {
      "page": "assessSamplesMinfiEwasWater",
      "title": "Assess sample quality before sample filtering",
      "topics": [
        "assessSamplesMinfiEwasWater"
      ]
    },
    {
      "page": "buildClockFoundationInputsPreprocessingPheno",
      "title": "Build Clock Foundation input tables from preprocessingPheno data",
      "topics": [
        "buildClockFoundationInputsPreprocessingPheno"
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    },
    {
      "page": "buildRawMinfiEwasWater",
      "title": "Build raw minfi preprocessing objects",
      "topics": [
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      "page": "collectSignificantCpGsMethylationGLM_T1",
      "title": "Collect significant CpG coefficient tables from fitted one-timepoint GLMs",
      "topics": [
        "collectSignificantCpGsMethylationGLM_T1"
      ]
    },
    {
      "page": "collectSignificantInteractionsMethylationGLMM_T1T2",
      "title": "Collect significant longitudinal model terms from fitted mixed-effects models",
      "topics": [
        "collectSignificantInteractionsMethylationGLMM_T1T2"
      ]
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    {
      "page": "combineTimepointsPreprocessingPheno",
      "title": "Combine selected timepoints for downstream longitudinal modeling",
      "topics": [
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      ]
    },
    {
      "page": "dnaEPICO",
      "title": "dnaEPICO: DNA methylation preprocessing and modeling workflows",
      "topics": [
        "dnaEPICO-package",
        "dnaEPICO"
      ]
    },
    {
      "page": "dnaEPICO_dnamReport_prepared-class",
      "title": "Result class returned by prepareDnamReportInputs",
      "topics": [
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        "dnaEPICO_dnamReport_prepared-class"
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    },
    {
      "page": "dnaEPICO_dnamReport_render-class",
      "title": "Result class returned by renderDnamReport",
      "topics": [
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        "dnaEPICO_dnamReport_render-class"
      ]
    },
    {
      "page": "dnaEPICO_dnamReport-class",
      "title": "Result class returned by dnamReport",
      "topics": [
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        "dnaEPICO_dnamReport-class"
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    },
    {
      "page": "dnaEPICO_methylationGLM_T1-class",
      "title": "Result class returned by methylationGLM_T1",
      "topics": [
        "dnaEPICO_methylationGLM_T1",
        "dnaEPICO_methylationGLM_T1-class"
      ]
    },
    {
      "page": "dnaEPICO_methylationGLMM_T1T2-class",
      "title": "Result class returned by methylationGLMM_T1T2",
      "topics": [
        "dnaEPICO_methylationGLMM_T1T2",
        "dnaEPICO_methylationGLMM_T1T2-class"
      ]
    },
    {
      "page": "dnaEPICO_preprocessingMinfiEwasWater-class",
      "title": "Result class returned by preprocessingMinfiEwasWater",
      "topics": [
        "dnaEPICO_preprocessingMinfiEwasWater",
        "dnaEPICO_preprocessingMinfiEwasWater-class"
      ]
    },
    {
      "page": "dnaEPICO_preprocessingPheno-class",
      "title": "Result class returned by preprocessingPheno",
      "topics": [
        "dnaEPICO_preprocessingPheno",
        "dnaEPICO_preprocessingPheno-class"
      ]
    },
    {
      "page": "dnaEPICO_svaEnmix-class",
      "title": "Result class returned by svaEnmix",
      "topics": [
        "dnaEPICO_svaEnmix",
        "dnaEPICO_svaEnmix-class"
      ]
    },
    {
      "page": "dnamReport",
      "title": "Generate a DNA methylation dashboard report",
      "topics": [
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      ]
    },
    {
      "page": "estimateLC",
      "title": "Estimate saliva cell proportions from DNA methylation beta values",
      "topics": [
        "estimateLC"
      ]
    },
    {
      "page": "estimateLCMinfiEwasWater",
      "title": "Estimate cell composition for preprocessingMinfiEwasWater",
      "topics": [
        "estimateLCMinfiEwasWater"
      ]
    },
    {
      "page": "estimateSvaEnmixControls",
      "title": "Estimate surrogate variables from ENmix control probes",
      "topics": [
        "estimateSvaEnmixControls"
      ]
    },
    {
      "page": "extractMake",
      "title": "Copy dnaEPICO Makefile to a user directory",
      "topics": [
        "extractMake"
      ]
    },
    {
      "page": "extractMetricsMinfiEwasWater",
      "title": "Extract beta, M, and copy-number matrices from a filtered object",
      "topics": [
        "extractMetricsMinfiEwasWater"
      ]
    },
    {
      "page": "filterProbesMinfiEwasWater",
      "title": "Filter probes from a normalized methylation object",
      "topics": [
        "filterProbesMinfiEwasWater"
      ]
    },
    {
      "page": "filterSamplesMinfiEwasWater",
      "title": "Filter failed samples from an RGSet and phenotype table",
      "topics": [
        "filterSamplesMinfiEwasWater"
      ]
    },
    {
      "page": "fitMethylationGLM_T1Models",
      "title": "Fit CpG-wise Gaussian GLMs for one-timepoint methylation analyses",
      "topics": [
        "fitMethylationGLM_T1Models"
      ]
    },
    {
      "page": "fitMethylationGLMM_T1T2Models",
      "title": "Fit CpG-wise mixed-effects models for longitudinal methylation analyses",
      "topics": [
        "fitMethylationGLMM_T1T2Models"
      ]
    },
    {
      "page": "loadMetricsPreprocessingPheno",
      "title": "Load methylation metric matrices for preprocessingPheno",
      "topics": [
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      ]
    },
    {
      "page": "mergeSvaTargetsEnmix",
      "title": "Merge surrogate variables into the phenotype table",
      "topics": [
        "mergeSvaTargetsEnmix"
      ]
    },
    {
      "page": "methylationGLM_T1",
      "title": "Fit CpG-wise GLMs for one-timepoint methylation analyses",
      "topics": [
        "methylationGLM_T1"
      ]
    },
    {
      "page": "methylationGLMM_T1T2",
      "title": "Fit CpG-wise linear mixed-effects models for longitudinal methylation analyses",
      "topics": [
        "methylationGLMM_T1T2"
      ]
    },
    {
      "page": "normalizeMinfiEwasWater",
      "title": "Normalize filtered samples with minfi and wateRmelon methods",
      "topics": [
        "normalizeMinfiEwasWater"
      ]
    },
    {
      "page": "plotAssessmentMinfiEwasWater",
      "title": "Plot quality-assessment outputs for preprocessingMinfiEwasWater",
      "topics": [
        "plotAssessmentMinfiEwasWater"
      ]
    },
    {
      "page": "plotCtrlMinfiEwasWater",
      "title": "Plot ENmix control images from an RGSet",
      "topics": [
        "plotCtrlMinfiEwasWater"
      ]
    },
    {
      "page": "plotMethylationGLM_T1Diagnostics",
      "title": "Plot diagnostic summaries for one-timepoint methylation GLMs",
      "topics": [
        "plotMethylationGLM_T1Diagnostics"
      ]
    },
    {
      "page": "plotMethylationGLM_T1Distributions",
      "title": "Plot phenotype and covariate distributions for one-timepoint GLM analyses",
      "topics": [
        "plotMethylationGLM_T1Distributions"
      ]
    },
    {
      "page": "plotMethylationGLMM_T1T2Diagnostics",
      "title": "Plot longitudinal mixed-effects model diagnostics",
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