LogNormalizedMatrix     Delayed log-normalization of a matrix
adt_quality_control     Quality control for ADT count data
adt_quality_control_defaults
                        Default parameters for ADT quality control
aggregateAcrossCells    Aggregate expression across cells
aggregateAcrossCells.se
                        Aggregate expression across cells in a
                        SummarizedExperiment
aggregateAcrossCellsDefaults
                        Default parameters for 'aggregateAcrossCells'
aggregateAcrossGenes    Aggregate expression across genes
aggregateAcrossGenes.se
                        Aggregate expression across gene sets in a
                        SummarizedExperiment
aggregateAcrossGenesDefaults
                        Default parameters for 'aggregateAcrossGenes'
analyze                 Defunct functions
analyze.se              Analyze single-cell data from a
                        SummarizedExperiment
buildSnnGraph           Build a shared nearest neighbor graph
buildSnnGraphDefaults   Default parameters for 'buildSnnGraph'
centerSizeFactors       Center size factors
centerSizeFactorsDefaults
                        Default parameters for 'centerSizeFactors'
centerSpikeInFactors    Center spike-in size factors
centerSpikeInFactorsDefaults
                        Default parameters for 'centerSpikeInFactors'
chooseHighlyVariableGenes
                        Choose highly variable genes
chooseHighlyVariableGenesDefaults
                        Default parameters for
                        'chooseHighlyVariableGenes'
choosePseudoCount       Choose a suitable pseudo-count
choosePseudoCountDefaults
                        Default parameters for 'choosePseudoCount'
chooseRnaHvgs.se        Choose highly variable genes from a
                        SummarizedExperiment
chooseRnaHvgsWithSpikeIns.se
                        Choose highly variable genes based on spike-ins
clusterGraph            Graph-based clustering of cells
clusterGraph.se         Graph-based clustering of cells in a
                        SingleCellExperiment
clusterGraphDefaults    Default parameters for 'clusterGraph'
clusterKmeans           K-means clustering
clusterKmeans.se        k-means clustering of cells in a
                        SingleCellExperiment
clusterKmeansDefaults   Default parameters for 'clusterKmeans'
combineFactors          Combine multiple factors
computeBlockWeights     Compute block weights
computeBlockWeightsDefaults
                        Default parameters for 'computeBlockWeights'
computeClrm1Factors     Compute size factors for ADT counts
computeClrm1FactorsDefaults
                        Default parameters for 'computeClrm1Factors'
correctMnn              Batch correction with mutual nearest neighbors
correctMnn.se           MNN correction on a SingleCellExperiment
correctMnnDefaults      Default parameters for 'correctMnn'
countGroupsByBlock      Count cells in groups and blocks
crispr_quality_control
                        Quality control for CRISPR count data
crispr_quality_control_defaults
                        Default parameters for CRISPR quality control
fitVarianceTrend        Fit a mean-variance trend
fitVarianceTrendDefaults
                        Default parameters for 'fitVarianceTrend'
getTestData.se          Get datasets for testing
modelGeneVariances      Model per-gene variances in expression
modelGeneVariancesDefaults
                        Default parameters for 'modelGeneVariances'
normalizeAdtCounts.se   Normalize ADT counts in a SummarizedExperiment
normalizeCounts         Normalize the count matrix
normalizeCountsDefaults
                        Default parameters for 'normalizeCounts'
normalizeCrisprCounts.se
                        Normalize CRISPR counts in a
                        SummarizedExperiment
normalizeRnaCounts.se   Normalize RNA counts in a SummarizedExperiment
normalizeRnaCountsWithSpikeIns.se
                        Normalize RNA and spike-in counts
quickAdtQc.se           Quick quality control for ADT data in a
                        SummarizedExperiment
quickCrisprQc.se        Quick quality control for CRISPR data in a
                        SummarizedExperiment
quickRnaQc.se           Quick quality control for RNA data in a
                        SummarizedExperiment
reportGroupMarkerStatistics
                        Report marker statistics for a single group
rna_quality_control     Quality control for RNA count data
rna_quality_control_defaults
                        Default parameters for RNA quality control
runAllNeighborSteps     Run all neighbor-related steps
runAllNeighborSteps.se
                        Run all nearest neighbor steps on a
                        SummarizedExperiment
runPca                  Principal components analysis
runPca.se               Principal components analysis of a
                        Summarizedexperiment
runPcaDefaults          Default parameters for 'runPca'
runTsne                 t-stochastic neighbor embedding
runTsne.se              t-SNE on a SummarizedExperiment
runTsneDefaults         Default parameters for 'runTsne'
runUmap                 Uniform manifold approximation and projection
runUmap.se              UMAP on a SummarizedExperiment
runUmapDefaults         Default parameters for 'runUmap'
sanitizeSizeFactors     Sanitize size factors
sanitizeSizeFactorsDefaults
                        Default parameters for 'sanitizeSizeFactors'
scaleByNeighbors        Scale and combine multiple embeddings
scaleByNeighbors.se     Scale and combine multiple embeddings in a
                        SingleCellExperiment
scaleByNeighborsDefaults
                        Default parameters for 'scaleByNeighbors'
scoreGeneSet            Score gene set activity for each cell
scoreGeneSet.se         Score a gene set in a SummarizedExperiment
scoreGeneSetDefaults    Default parameters for 'scoreGeneSet'
scoreMarkers            Score marker genes
scoreMarkers.se         Score marker genes in a SummarizedExperiment
scoreMarkersDefaults    Default parameters for 'scoreMarkers'
scrapper-package        scrapper: Bindings to C++ Libraries for
                        Single-Cell Analysis
subsampleByNeighbors    Subsample cells based on their neighbors
subsampleByNeighborsDefaults
                        Default parameters for 'subsampleByNeighbors'
subsampleByPartition    Subsample by partition
subsampleByPartitionDefaults
                        Default parameters for 'subsampleByPartition'
summarizeEffects        Summarize pairwise effect sizes for each group
summarizeEffectsDefaults
                        Default parameters for
                        'summarizeEffectsDefaults'
testEnrichment          Test for gene set enrichment
testEnrichmentDefaults
                        Default parameters for 'testEnrichment'
