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  "Title": "Chromatin Variation Across Regions",
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  "Description": "Determine variation in chromatin accessibility across sets\nof annotations or peaks. Designed primarily for single-cell or\nsparse chromatin accessibility data, e.g. from scATAC-seq or\nsparse bulk ATAC or DNAse-seq experiments.",
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    "annotationMatches",
    "annotationMatches<-",
    "assembleKmers",
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    "chromVAR_theme",
    "computeDeviations",
    "computeExpectations",
    "computeVariability",
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    "deviationScores",
    "deviationsCovariability",
    "deviationsTsne",
    "differentialDeviations",
    "differentialVariability",
    "filterPeaks",
    "filterSamples",
    "filterSamplesPlot",
    "getAnnotationCorrelation",
    "getAnnotations",
    "getAnnotationSynergy",
    "getBackgroundPeaks",
    "getCisGroups",
    "getCounts",
    "getFragmentsPerPeak",
    "getFragmentsPerSample",
    "getJasparMotifs",
    "getPeaks",
    "getPermutedData",
    "getSampleCorrelation",
    "getSampleDepths",
    "getSampleDistance",
    "getTotalFragments",
    "makeBiasBins",
    "makePermutedSets",
    "matchKmers",
    "plotDeviationsTsne",
    "plotKmerMismatch",
    "plotVariability",
    "pwmDistance",
    "rbind",
    "readNarrowpeaks"
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      "title": "example_counts",
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      "fields": [],
      "table": false,
      "tojson": false
    },
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      "object": "mini_counts",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "mini_dev",
      "title": "mini_dev",
      "object": "mini_dev",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mini_ix",
      "title": "mini_ix",
      "object": "mini_ix",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
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    {
      "page": "addGCBias",
      "title": "addGCBias",
      "topics": [
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        "addGCBias,RangedSummarizedExperiment-method",
        "addGCBias,SummarizedExperiment-method"
      ]
    },
    {
      "page": "annotationMatches",
      "title": "annotationMatches",
      "topics": [
        "annoation_matches<-,SummarizedExperiment-method",
        "annotationMatches",
        "annotationMatches,SummarizedExperiment-method",
        "annotationMatches<-",
        "annotationMatches<-,SummarizedExperiment-method"
      ]
    },
    {
      "page": "assembleKmers",
      "title": "assembleKmers",
      "topics": [
        "assembleKmers"
      ]
    },
    {
      "page": "cbind-chromVARDeviations-method",
      "title": "cbind method for chromVARDeviations",
      "topics": [
        "cbind,chromVARDeviations-method"
      ]
    },
    {
      "page": "chromVAR",
      "title": "chromVAR: A package for computing variability across sets of peaks.",
      "topics": [
        "chromVAR-package",
        "chromVAR"
      ]
    },
    {
      "page": "chromVAR_theme",
      "title": "chromVAR_theme",
      "topics": [
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      ]
    },
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      "title": "chromVARDeviations",
      "topics": [
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    },
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      "page": "computeDeviations",
      "title": "computeDeviations",
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        "computeDeviations,MatrixOrmatrix,list-method",
        "computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method",
        "computeDeviations,MatrixOrmatrix,missingOrNULL-method",
        "computeDeviations,MatrixOrmatrix,SummarizedExperiment-method",
        "computeDeviations,SummarizedExperiment,list-method",
        "computeDeviations,SummarizedExperiment,MatrixOrmatrix-method",
        "computeDeviations,SummarizedExperiment,missingOrNULL-method",
        "computeDeviations,SummarizedExperiment,SummarizedExperiment-method"
      ]
    },
    {
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      "title": "computeExpectations",
      "topics": [
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        "computeExpectations,MatrixOrmatrix-method",
        "computeExpectations,SummarizedExperiment-method"
      ]
    },
    {
      "page": "computeVariability",
      "title": "computeVariability",
      "topics": [
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      ]
    },
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      "title": "Accessors for the 'counts' slot of a SummarizedExperiment",
      "topics": [
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        "counts<-,SummarizedExperiment,MatrixOrmatrix-method",
        "counts<-,SummarizedExperiment-method"
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    },
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      "page": "deviations",
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      "topics": [
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        "deviations,chromVARDeviations-method"
      ]
    },
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      "page": "deviationScores",
      "title": "deviationScores",
      "topics": [
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        "deviationScores,chromVARDeviations-method"
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    },
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      "title": "deviationsCovariability",
      "topics": [
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      "title": "deviationsTsne",
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      "page": "differentialDeviations",
      "title": "differentialDeviations",
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    {
      "page": "differentialVariability",
      "title": "differentialVariability",
      "topics": [
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      "title": "example_counts",
      "topics": [
        "example_counts"
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    },
    {
      "page": "filterPeaks",
      "title": "filterPeaks",
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      "page": "getAnnotationCorrelation",
      "title": "getAnnotationCorrelation",
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        "getAnnotationCorrelation,MatrixOrmatrix,list-method",
        "getAnnotationCorrelation,MatrixOrmatrix,MatrixOrmatrix-method",
        "getAnnotationCorrelation,MatrixOrmatrix,SummarizedExperiment-method",
        "getAnnotationCorrelation,SummarizedExperiment,list-method",
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      "page": "getAnnotations",
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        "getAnnotations",
        "getAnnotations,character-method",
        "getAnnotations,data.frame-method",
        "getAnnotations,GRangesList-method",
        "getAnnotations,list-method",
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    {
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        "getAnnotationSynergy,MatrixOrmatrix,list-method",
        "getAnnotationSynergy,MatrixOrmatrix,MatrixOrmatrix-method",
        "getAnnotationSynergy,MatrixOrmatrix,SummarizedExperiment-method",
        "getAnnotationSynergy,SummarizedExperiment,list-method",
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        "getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getBackgroundPeaks",
      "title": "getBackgroundPeaks",
      "topics": [
        "getBackgroundPeaks",
        "getBackgroundPeaks,MatrixOrmatrix-method",
        "getBackgroundPeaks,RangedSummarizedExperiment-method",
        "getBackgroundPeaks,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getCisGroups",
      "title": "getCisGroups",
      "topics": [
        "getCisGroups",
        "getCisGroups,GenomicRanges-method",
        "getCisGroups,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "getCounts",
      "title": "getCounts",
      "topics": [
        "getCounts"
      ]
    },
    {
      "page": "getFragmentsPerPeak",
      "title": "getFragmentsPerPeak",
      "topics": [
        "getFragmentsPerPeak",
        "getFragmentsPerPeak,MatrixOrmatrix-method",
        "getFragmentsPerPeak,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getFragmentsPerSample",
      "title": "getFragmentsPerSample",
      "topics": [
        "getFragmentsPerSample",
        "getFragmentsPerSample,MatrixOrmatrix-method",
        "getFragmentsPerSample,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getJasparMotifs",
      "title": "getJasparMotifs",
      "topics": [
        "getJasparMotifs"
      ]
    },
    {
      "page": "getPeaks",
      "title": "getPeaks",
      "topics": [
        "getPeaks"
      ]
    },
    {
      "page": "getPermutedData",
      "title": "getPermutedData",
      "topics": [
        "getPermutedData"
      ]
    },
    {
      "page": "getSampleCorrelation",
      "title": "getSampleCorrelation",
      "topics": [
        "getSampleCorrelation"
      ]
    },
    {
      "page": "getSampleDepths",
      "title": "getSampleDepths",
      "topics": [
        "getSampleDepths"
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    },
    {
      "page": "getSampleDistance",
      "title": "getSampleDistance",
      "topics": [
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    },
    {
      "page": "getTotalFragments",
      "title": "getTotalFragments",
      "topics": [
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        "getTotalFragments,MatrixOrmatrix-method",
        "getTotalFragments,SummarizedExperiment-method"
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      "page": "makeBiasBins",
      "title": "makeBiasBins",
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        "makeBiasBins,MatrixOrmatrix-method",
        "makeBiasBins,RangedSummarizedExperiment-method",
        "makeBiasBins,SummarizedExperiment-method"
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    {
      "page": "makePermutedSets",
      "title": "makePermutedSets",
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        "makePermutedSets,MatrixOrmatrix,list-method",
        "makePermutedSets,MatrixOrmatrix,MatrixOrmatrix-method",
        "makePermutedSets,MatrixOrmatrix,SummarizedExperiment-method",
        "makePermutedSets,RangedSummarizedExperiment,list-method",
        "makePermutedSets,RangedSummarizedExperiment,MatrixOrmatrix-method",
        "makePermutedSets,RangedSummarizedExperiment,SummarizedExperiment-method",
        "makePermutedSets,SummarizedExperiment,list-method",
        "makePermutedSets,SummarizedExperiment,MatrixOrmatrix-method",
        "makePermutedSets,SummarizedExperiment,SummarizedExperiment-method"
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    },
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      "page": "matchKmers",
      "title": "matchKmers",
      "topics": [
        "matchKmers",
        "matchKmers,character,character-method",
        "matchKmers,character,DNAString-method",
        "matchKmers,character,DNAStringSet-method",
        "matchKmers,character,GenomicRanges-method",
        "matchKmers,character,RangedSummarizedExperiment-method",
        "matchKmers,DNAString,ANY-method",
        "matchKmers,DNAStringSet,ANY-method",
        "matchKmers,numeric,ANY-method"
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    {
      "page": "mini_counts",
      "title": "mini_counts",
      "topics": [
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    {
      "page": "mini_dev",
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