adt_quality_control     Quality control for ADT count data
aggregateAcrossCells    Aggregate expression across cells
aggregateAcrossGenes    Aggregate expression across genes
analyze                 Analyze single-cell data
buildSnnGraph           Build a shared nearest neighbor graph
centerSizeFactors       Center size factors
chooseHighlyVariableGenes
                        Choose highly variable genes
choosePseudoCount       Choose a suitable pseudo-count
clusterGraph            Graph-based clustering of cells
clusterKmeans           K-means clustering
combineFactors          Combine multiple factors
computeClrm1Factors     Compute size factors for ADT counts
convertAnalyzeResults   Convert analysis results into a
                        SingleCellExperiment
correctMnn              Batch correction with mutual nearest neighbors
crispr_quality_control
                        Quality control for CRISPR count data
fitVarianceTrend        Fit a mean-variance trend
modelGeneVariances      Model per-gene variances in expression
normalizeCounts         Normalize the count matrix
reportGroupMarkerStatistics
                        Report marker statistics for a single group
rna_quality_control     Quality control for RNA count data
runAllNeighborSteps     Run all neighbor-related steps
runPca                  Principal components analysis
runTsne                 t-stochastic neighbor embedding
runUmap                 Uniform manifold approxation and projection
sanitizeSizeFactors     Sanitize size factors
scaleByNeighbors        Scale and combine multiple embeddings
scoreGeneSet            Score gene set activity for each cell
scoreMarkers            Score marker genes
subsampleByNeighbors    Subsample cells based on their neighbors
summarizeEffects        Summarize pairwise effect sizes for each group
testEnrichment          Test for gene set enrichment
