adt_quality_control     Quality control for ADT count data
aggregateAcrossCells    Aggregate expression across cells
aggregateAcrossCells.se
                        Aggregate expression across cells in a
                        SummarizedExperiment
aggregateAcrossGenes    Aggregate expression across genes
aggregateAcrossGenes.se
                        Aggregate expression across gene sets in a
                        SummarizedExperiment
analyze                 Analyze single-cell data
analyze.se              Analyze single-cell data from a
                        SummarizedExperiment
buildSnnGraph           Build a shared nearest neighbor graph
centerSizeFactors       Center size factors
chooseHighlyVariableGenes
                        Choose highly variable genes
choosePseudoCount       Choose a suitable pseudo-count
chooseRnaHvgs.se        Choose highly variable genes from a
                        SummarizedExperiment
clusterGraph            Graph-based clustering of cells
clusterGraph.se         Graph-based clustering of cells in a
                        SingleCellExperiment
clusterKmeans           K-means clustering
clusterKmeans.se        k-means clustering of cells in a
                        SingleCellExperiment
combineFactors          Combine multiple factors
computeBlockWeights     Compute block weights
computeClrm1Factors     Compute size factors for ADT counts
convertAnalyzeResults   Convert analysis results into a
                        SingleCellExperiment
correctMnn              Batch correction with mutual nearest neighbors
correctMnn.se           MNN correction on a SingleCellExperiment
countGroupsByBlock      Count cells in groups and blocks
crispr_quality_control
                        Quality control for CRISPR count data
fitVarianceTrend        Fit a mean-variance trend
getTestData.se          Get datasets for testing
LogNormalizedMatrix     Delayed log-normalization of a matrix
modelGeneVariances      Model per-gene variances in expression
normalizeAdtCounts.se   Normalize ADT counts in a SummarizedExperiment
normalizeCounts         Normalize the count matrix
normalizeCrisprCounts.se
                        Normalize CRISPR counts in a
                        SummarizedExperiment
normalizeRnaCounts.se   Normalize RNA counts in a SummarizedExperiment
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
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
runTsne                 t-stochastic neighbor embedding
runTsne.se              t-SNE on a SummarizedExperiment
runUmap                 Uniform manifold approximation and projection
runUmap.se              UMAP on a SummarizedExperiment
sanitizeSizeFactors     Sanitize size factors
scaleByNeighbors        Scale and combine multiple embeddings
scaleByNeighbors.se     Scale and combine multiple embeddings in a
                        SingleCellExperiment
scoreGeneSet            Score gene set activity for each cell
scoreGeneSet.se         Score a gene set in a SummarizedExperiment
scoreMarkers            Score marker genes
scoreMarkers.se         Score marker genes in a SummarizedExperiment
scrapper-package        scrapper: Bindings to C++ Libraries for
                        Single-Cell Analysis
subsampleByNeighbors    Subsample cells based on their neighbors
summarizeEffects        Summarize pairwise effect sizes for each group
testEnrichment          Test for gene set enrichment
