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  "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"cre\", \"aut\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
  "Title": "Bindings to C++ Libraries for Single-Cell Analysis",
  "Description": "Implements R bindings to C++ code for analyzing\nsingle-cell (expression) data, mostly from various libscran\nlibraries. Each function performs an individual step in the\nsingle-cell analysis workflow, ranging from quality control to\nclustering and marker detection. Additional wrappers are\nprovided for easy construction of end-to-end workflows\ninvolving Bioconductor objects like SingleCellExperiments.",
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  "biocViews": "Normalization, RNASeq, Software, GeneExpression,\nTranscriptomics, SingleCell, BatchEffect, QualityControl,\nDifferentialExpression, FeatureExtraction, PrincipalComponent,\nClustering",
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  "Author": "Aaron Lun [cre, aut]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
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    "aggregateAcrossCellsDefaults",
    "aggregateAcrossGenes",
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    "aggregateAcrossGenesDefaults",
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    "centerSpikeInFactors",
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    "chooseHighlyVariableGenes",
    "chooseHighlyVariableGenesDefaults",
    "choosePseudoCount",
    "choosePseudoCountDefaults",
    "chooseRnaHvgs.se",
    "chooseRnaHvgsWithSpikeIns.se",
    "clusterGraph",
    "clusterGraph.se",
    "clusterGraphDefaults",
    "clusterKmeans",
    "clusterKmeans.se",
    "clusterKmeansDefaults",
    "combineFactors",
    "computeAdtQcMetrics",
    "computeAdtQcMetricsDefaults",
    "computeBlockWeights",
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    "computeClrm1Factors",
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    "computeCrisprQcMetrics",
    "computeCrisprQcMetricsDefaults",
    "computeRnaQcMetrics",
    "computeRnaQcMetricsDefaults",
    "computeRnaQcMetricsWithAltExps",
    "convertAnalyzeResults",
    "correctMnn",
    "correctMnn.se",
    "correctMnnDefaults",
    "countGroupsByBlock",
    "DelayedArray",
    "extract_array",
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    "filterAdtQcMetrics",
    "filterCrisprQcMetrics",
    "filterRnaQcMetrics",
    "fitVarianceTrend",
    "fitVarianceTrendDefaults",
    "formatComputeAdtQcMetricsResult",
    "formatComputeCrisprQcMetricsResult",
    "formatComputeRnaQcMetricsResult",
    "formatModelGeneVariancesResult",
    "formatScoreMarkersResult",
    "getTestAdtData.se",
    "getTestCrisprData.se",
    "getTestRnaData.se",
    "initializeCpp",
    "is_sparse",
    "LogNormalizedMatrix",
    "LogNormalizedMatrixSeed",
    "modelGeneVariances",
    "modelGeneVariancesDefaults",
    "normalizeAdtCounts.se",
    "normalizeCounts",
    "normalizeCountsDefaults",
    "normalizeCrisprCounts.se",
    "normalizeRnaCounts.se",
    "normalizeRnaCountsWithSpikeIns.se",
    "previewMarkers",
    "quickAdtQc.se",
    "quickCrisprQc.se",
    "quickRnaQc.se",
    "reportGroupMarkerStatistics",
    "runAllNeighborSteps",
    "runAllNeighborSteps.se",
    "runPca",
    "runPca.se",
    "runPcaDefaults",
    "runTsne",
    "runTsne.se",
    "runTsneDefaults",
    "runUmap",
    "runUmap.se",
    "runUmapDefaults",
    "sanitizeSizeFactors",
    "sanitizeSizeFactorsDefaults",
    "scaleByNeighbors",
    "scaleByNeighbors.se",
    "scaleByNeighborsDefaults",
    "scoreGeneSet",
    "scoreGeneSet.se",
    "scoreGeneSetDefaults",
    "scoreMarkers",
    "scoreMarkers.se",
    "scoreMarkersDefaults",
    "subsampleByNeighbors",
    "subsampleByNeighborsDefaults",
    "subsampleByPartition",
    "subsampleByPartitionDefaults",
    "suggestAdtQcThresholds",
    "suggestAdtQcThresholdsDefaults",
    "suggestCrisprQcThresholds",
    "suggestCrisprQcThresholdsDefaults",
    "suggestRnaQcThresholds",
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    "summarizeEffects",
    "summarizeEffectsDefaults",
    "testEnrichment",
    "testEnrichmentDefaults",
    "tsnePerplexityToNeighbors",
    "type"
  ],
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      "title": "scrapper: Bindings to C++ Libraries for Single-Cell Analysis",
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        "scrapper-package",
        "scrapper"
      ]
    },
    {
      "page": "adt_quality_control",
      "title": "Quality control for ADT count data",
      "topics": [
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        "computeAdtQcMetrics",
        "filterAdtQcMetrics",
        "suggestAdtQcThresholds"
      ]
    },
    {
      "page": "adt_quality_control_defaults",
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        "computeAdtQcMetricsDefaults",
        "suggestAdtQcThresholdsDefaults"
      ]
    },
    {
      "page": "aggregateAcrossCells",
      "title": "Aggregate expression across cells",
      "topics": [
        "aggregateAcrossCells"
      ]
    },
    {
      "page": "aggregateAcrossCells.se",
      "title": "Aggregate expression across cells in a SummarizedExperiment",
      "topics": [
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        "aggregateColData"
      ]
    },
    {
      "page": "aggregateAcrossCellsDefaults",
      "title": "Default parameters for 'aggregateAcrossCells'",
      "topics": [
        "aggregateAcrossCellsDefaults"
      ]
    },
    {
      "page": "aggregateAcrossGenes",
      "title": "Aggregate expression across genes",
      "topics": [
        "aggregateAcrossGenes"
      ]
    },
    {
      "page": "aggregateAcrossGenes.se",
      "title": "Aggregate expression across gene sets in a SummarizedExperiment",
      "topics": [
        "aggregateAcrossGenes.se"
      ]
    },
    {
      "page": "aggregateAcrossGenesDefaults",
      "title": "Default parameters for 'aggregateAcrossGenes'",
      "topics": [
        "aggregateAcrossGenesDefaults"
      ]
    },
    {
      "page": "defunct",
      "title": "Defunct functions",
      "topics": [
        "analyze",
        "convertAnalyzeResults"
      ]
    },
    {
      "page": "analyze.se",
      "title": "Analyze single-cell data from a SummarizedExperiment",
      "topics": [
        "analyze.se"
      ]
    },
    {
      "page": "buildSnnGraph",
      "title": "Build a shared nearest neighbor graph",
      "topics": [
        "buildSnnGraph"
      ]
    },
    {
      "page": "buildSnnGraphDefaults",
      "title": "Default parameters for 'buildSnnGraph'",
      "topics": [
        "buildSnnGraphDefaults"
      ]
    },
    {
      "page": "centerSizeFactors",
      "title": "Center size factors",
      "topics": [
        "centerSizeFactors"
      ]
    },
    {
      "page": "centerSizeFactorsDefaults",
      "title": "Default parameters for 'centerSizeFactors'",
      "topics": [
        "centerSizeFactorsDefaults"
      ]
    },
    {
      "page": "centerSpikeInFactors",
      "title": "Center spike-in size factors",
      "topics": [
        "centerSpikeInFactors"
      ]
    },
    {
      "page": "centerSpikeInFactorsDefaults",
      "title": "Default parameters for 'centerSpikeInFactors'",
      "topics": [
        "centerSpikeInFactorsDefaults"
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    },
    {
      "page": "chooseHighlyVariableGenes",
      "title": "Choose highly variable genes",
      "topics": [
        "chooseHighlyVariableGenes"
      ]
    },
    {
      "page": "chooseHighlyVariableGenesDefaults",
      "title": "Default parameters for 'chooseHighlyVariableGenes'",
      "topics": [
        "chooseHighlyVariableGenesDefaults"
      ]
    },
    {
      "page": "choosePseudoCount",
      "title": "Choose a suitable pseudo-count",
      "topics": [
        "choosePseudoCount"
      ]
    },
    {
      "page": "choosePseudoCountDefaults",
      "title": "Default parameters for 'choosePseudoCount'",
      "topics": [
        "choosePseudoCountDefaults"
      ]
    },
    {
      "page": "chooseRnaHvgs.se",
      "title": "Choose highly variable genes from a SummarizedExperiment",
      "topics": [
        "chooseRnaHvgs.se",
        "formatModelGeneVariancesResult"
      ]
    },
    {
      "page": "chooseRnaHvgsWithSpikeIns.se",
      "title": "Choose highly variable genes based on spike-ins",
      "topics": [
        "chooseRnaHvgsWithSpikeIns.se"
      ]
    },
    {
      "page": "clusterGraph",
      "title": "Graph-based clustering of cells",
      "topics": [
        "clusterGraph"
      ]
    },
    {
      "page": "clusterGraph.se",
      "title": "Graph-based clustering of cells in a SingleCellExperiment",
      "topics": [
        "clusterGraph.se"
      ]
    },
    {
      "page": "clusterGraphDefaults",
      "title": "Default parameters for 'clusterGraph'",
      "topics": [
        "clusterGraphDefaults"
      ]
    },
    {
      "page": "clusterKmeans",
      "title": "K-means clustering",
      "topics": [
        "clusterKmeans"
      ]
    },
    {
      "page": "clusterKmeans.se",
      "title": "k-means clustering of cells in a SingleCellExperiment",
      "topics": [
        "clusterKmeans.se"
      ]
    },
    {
      "page": "clusterKmeansDefaults",
      "title": "Default parameters for 'clusterKmeans'",
      "topics": [
        "clusterKmeansDefaults"
      ]
    },
    {
      "page": "combineFactors",
      "title": "Combine multiple factors",
      "topics": [
        "combineFactors"
      ]
    },
    {
      "page": "computeBlockWeights",
      "title": "Compute block weights",
      "topics": [
        "computeBlockWeights"
      ]
    },
    {
      "page": "computeBlockWeightsDefaults",
      "title": "Default parameters for 'computeBlockWeights'",
      "topics": [
        "computeBlockWeightsDefaults"
      ]
    },
    {
      "page": "computeClrm1Factors",
      "title": "Compute size factors for ADT counts",
      "topics": [
        "computeClrm1Factors"
      ]
    },
    {
      "page": "computeClrm1FactorsDefaults",
      "title": "Default parameters for 'computeClrm1Factors'",
      "topics": [
        "computeClrm1FactorsDefaults"
      ]
    },
    {
      "page": "correctMnn",
      "title": "Batch correction with mutual nearest neighbors",
      "topics": [
        "correctMnn"
      ]
    },
    {
      "page": "correctMnn.se",
      "title": "MNN correction on a SingleCellExperiment",
      "topics": [
        "correctMnn.se"
      ]
    },
    {
      "page": "correctMnnDefaults",
      "title": "Default parameters for 'correctMnn'",
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