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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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  "Date/Publication": "2026-05-19 10:09:14 UTC",
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    "aggregateAcrossCells.se",
    "aggregateAcrossGenes",
    "aggregateAcrossGenes.se",
    "aggregateColData",
    "analyze",
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    "clusterGraph",
    "clusterGraph.se",
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    "combineFactors",
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    "computeBlockWeights",
    "computeClrm1Factors",
    "computeCrisprQcMetrics",
    "computeRnaQcMetrics",
    "computeRnaQcMetricsWithAltExps",
    "convertAnalyzeResults",
    "correctMnn",
    "correctMnn.se",
    "countGroupsByBlock",
    "DelayedArray",
    "extract_array",
    "extract_sparse_array",
    "filterAdtQcMetrics",
    "filterCrisprQcMetrics",
    "filterRnaQcMetrics",
    "fitVarianceTrend",
    "formatComputeAdtQcMetricsResult",
    "formatComputeCrisprQcMetricsResult",
    "formatComputeRnaQcMetricsResult",
    "formatModelGeneVariancesResult",
    "formatScoreMarkersResult",
    "getTestAdtData.se",
    "getTestCrisprData.se",
    "getTestRnaData.se",
    "initializeCpp",
    "is_sparse",
    "LogNormalizedMatrix",
    "LogNormalizedMatrixSeed",
    "modelGeneVariances",
    "normalizeAdtCounts.se",
    "normalizeCounts",
    "normalizeCrisprCounts.se",
    "normalizeRnaCounts.se",
    "previewMarkers",
    "quickAdtQc.se",
    "quickCrisprQc.se",
    "quickRnaQc.se",
    "reportGroupMarkerStatistics",
    "runAllNeighborSteps",
    "runAllNeighborSteps.se",
    "runPca",
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    "runTsne",
    "runTsne.se",
    "runUmap",
    "runUmap.se",
    "sanitizeSizeFactors",
    "scaleByNeighbors",
    "scaleByNeighbors.se",
    "scoreGeneSet",
    "scoreGeneSet.se",
    "scoreMarkers",
    "scoreMarkers.se",
    "subsampleByNeighbors",
    "suggestAdtQcThresholds",
    "suggestCrisprQcThresholds",
    "suggestRnaQcThresholds",
    "summarizeEffects",
    "testEnrichment",
    "tsnePerplexityToNeighbors",
    "type"
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    {
      "page": "scrapper-package",
      "title": "scrapper: Bindings to C++ Libraries for Single-Cell Analysis",
      "topics": [
        "scrapper-package",
        "scrapper"
      ]
    },
    {
      "page": "adt_quality_control",
      "title": "Quality control for ADT count data",
      "topics": [
        "adt_quality_control",
        "computeAdtQcMetrics",
        "filterAdtQcMetrics",
        "suggestAdtQcThresholds"
      ]
    },
    {
      "page": "aggregateAcrossCells",
      "title": "Aggregate expression across cells",
      "topics": [
        "aggregateAcrossCells"
      ]
    },
    {
      "page": "aggregateAcrossCells.se",
      "title": "Aggregate expression across cells in a SummarizedExperiment",
      "topics": [
        "aggregateAcrossCells.se",
        "aggregateColData"
      ]
    },
    {
      "page": "aggregateAcrossGenes",
      "title": "Aggregate expression across genes",
      "topics": [
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      ]
    },
    {
      "page": "aggregateAcrossGenes.se",
      "title": "Aggregate expression across gene sets in a SummarizedExperiment",
      "topics": [
        "aggregateAcrossGenes.se"
      ]
    },
    {
      "page": "analyze",
      "title": "Analyze single-cell data",
      "topics": [
        "analyze"
      ]
    },
    {
      "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": "centerSizeFactors",
      "title": "Center size factors",
      "topics": [
        "centerSizeFactors"
      ]
    },
    {
      "page": "chooseHighlyVariableGenes",
      "title": "Choose highly variable genes",
      "topics": [
        "chooseHighlyVariableGenes"
      ]
    },
    {
      "page": "choosePseudoCount",
      "title": "Choose a suitable pseudo-count",
      "topics": [
        "choosePseudoCount"
      ]
    },
    {
      "page": "chooseRnaHvgs.se",
      "title": "Choose highly variable genes from a SummarizedExperiment",
      "topics": [
        "chooseRnaHvgs.se",
        "formatModelGeneVariancesResult"
      ]
    },
    {
      "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": "clusterKmeans",
      "title": "K-means clustering",
      "topics": [
        "clusterKmeans"
      ]
    },
    {
      "page": "clusterKmeans.se",
      "title": "k-means clustering of cells in a SingleCellExperiment",
      "topics": [
        "clusterKmeans.se"
      ]
    },
    {
      "page": "combineFactors",
      "title": "Combine multiple factors",
      "topics": [
        "combineFactors"
      ]
    },
    {
      "page": "computeBlockWeights",
      "title": "Compute block weights",
      "topics": [
        "computeBlockWeights"
      ]
    },
    {
      "page": "computeClrm1Factors",
      "title": "Compute size factors for ADT counts",
      "topics": [
        "computeClrm1Factors"
      ]
    },
    {
      "page": "convertAnalyzeResults",
      "title": "Convert analysis results into a SingleCellExperiment",
      "topics": [
        "convertAnalyzeResults"
      ]
    },
    {
      "page": "correctMnn",
      "title": "Batch correction with mutual nearest neighbors",
      "topics": [
        "correctMnn"
      ]
    },
    {
      "page": "correctMnn.se",
      "title": "MNN correction on a SingleCellExperiment",
      "topics": [
        "correctMnn.se"
      ]
    },
    {
      "page": "countGroupsByBlock",
      "title": "Count cells in groups and blocks",
      "topics": [
        "countGroupsByBlock"
      ]
    },
    {
      "page": "crispr_quality_control",
      "title": "Quality control for CRISPR count data",
      "topics": [
        "computeCrisprQcMetrics",
        "crispr_quality_control",
        "filterCrisprQcMetrics",
        "suggestCrisprQcThresholds"
      ]
    },
    {
      "page": "fitVarianceTrend",
      "title": "Fit a mean-variance trend",
      "topics": [
        "fitVarianceTrend"
      ]
    },
    {
      "page": "getTestData.se",
      "title": "Get datasets for testing",
      "topics": [
        "getTestAdtData.se",
        "getTestCrisprData.se",
        "getTestData.se",
        "getTestRnaData.se"
      ]
    },
    {
      "page": "LogNormalizedMatrix",
      "title": "Delayed log-normalization of a matrix",
      "topics": [
        "DelayedArray,LogNormalizedMatrixSeed-method",
        "dim,LogNormalizedMatrixSeed-method",
        "dimnames,LogNormalizedMatrixSeed-method",
        "extract_array,LogNormalizedMatrixSeed-method",
        "extract_sparse_array,LogNormalizedMatrixSeed-method",
        "initializeCpp,LogNormalizedMatrixSeed-method",
        "is_sparse,LogNormalizedMatrixSeed-method",
        "LogNormalizedMatrix",
        "LogNormalizedMatrix-class",
        "LogNormalizedMatrixSeed",
        "LogNormalizedMatrixSeed-class",
        "matrixClass,LogNormalizedMatrixSeed-method",
        "type,LogNormalizedMatrixSeed-method"
      ]
    },
    {
      "page": "modelGeneVariances",
      "title": "Model per-gene variances in expression",
      "topics": [
        "modelGeneVariances"
      ]
    },
    {
      "page": "normalizeAdtCounts.se",
      "title": "Normalize ADT counts in a SummarizedExperiment",
      "topics": [
        "normalizeAdtCounts.se"
      ]
    },
    {
      "page": "normalizeCounts",
      "title": "Normalize the count matrix",
      "topics": [
        "normalizeCounts"
      ]
    },
    {
      "page": "normalizeCrisprCounts.se",
      "title": "Normalize CRISPR counts in a SummarizedExperiment",
      "topics": [
        "normalizeCrisprCounts.se"
      ]
    },
    {
      "page": "normalizeRnaCounts.se",
      "title": "Normalize RNA counts in a SummarizedExperiment",
      "topics": [
        "normalizeRnaCounts.se"
      ]
    },
    {
      "page": "quickAdtQc.se",
      "title": "Quick quality control for ADT data in a SummarizedExperiment",
      "topics": [
        "formatComputeAdtQcMetricsResult",
        "quickAdtQc.se"
      ]
    },
    {
      "page": "quickCrisprQc.se",
      "title": "Quick quality control for CRISPR data in a SummarizedExperiment",
      "topics": [
        "formatComputeCrisprQcMetricsResult",
        "quickCrisprQc.se"
      ]
    },
    {
      "page": "quickRnaQc.se",
      "title": "Quick quality control for RNA data in a SummarizedExperiment",
      "topics": [
        "computeRnaQcMetricsWithAltExps",
        "formatComputeRnaQcMetricsResult",
        "quickRnaQc.se"
      ]
    },
    {
      "page": "reportGroupMarkerStatistics",
      "title": "Report marker statistics for a single group",
      "topics": [
        "reportGroupMarkerStatistics"
      ]
    },
    {
      "page": "rna_quality_control",
      "title": "Quality control for RNA count data",
      "topics": [
        "computeRnaQcMetrics",
        "filterRnaQcMetrics",
        "rna_quality_control",
        "suggestRnaQcThresholds"
      ]
    },
    {
      "page": "runAllNeighborSteps",
      "title": "Run all neighbor-related steps",
      "topics": [
        "runAllNeighborSteps"
      ]
    },
    {
      "page": "runAllNeighborSteps.se",
      "title": "Run all nearest neighbor steps on a SummarizedExperiment",
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