boxplotPCA              Plot Principal Components for Different Cell
                        Types
calculateCategorizationEntropy
                        Calculate Categorization Entropy
calculateCellDistancesSimilarity
                        Function to Calculate Bhattacharyya
                        Coefficients and Hellinger Distances
calculateCramerPValue   Calculate Cramer Test P-Values for Two-Sample
                        Comparison of Multivariate ECDFs
calculateDiscriminantSpace
                        Project Query Data onto a Unified Discriminant
                        Space of Reference Data
calculateGraphIntegration
                        Calculate Graph Community Integration
                        Diagnostics
calculateHVGOverlap     Calculate the Overlap Coefficient for Highly
                        Variable Genes
calculateHotellingPValue
                        Perform Hotelling's T-squared Test on PCA
                        Scores for Single-cell RNA-seq Data
calculateMMDPValue      Calculate Maximum Mean Discrepancy P-Values for
                        Two-Sample Comparison
calculateSIRSpace       Calculate Sliced Inverse Regression (SIR) Space
                        for Different Cell Types
calculateTopLoadingGeneShifts
                        Calculate Top Loading Gene Expression Shifts
calculateVarImpOverlap
                        Compare Gene Importance Across Datasets Using
                        Random Forest
comparePCA              Compare Principal Components Analysis (PCA)
                        Results
detectAnomaly           PCA Anomaly Scores via Isolation Forests with
                        Visualization
histQCvsAnnotation      Histograms: QC Stats and Annotation Scores
                        Visualization
plot.regressPCObject    Plot Regression Results on Principal Components
plotCellTypeMDS         Plot Reference and Query Cell Types using MDS
plotCellTypePCA         Plot Principal Components for Different Cell
                        Types
plotGeneExpressionDimred
                        Visualize gene expression on a dimensional
                        reduction plot
plotGeneSetScores       Visualization of gene sets or pathway scores on
                        dimensional reduction plot
plotMarkerExpression    Plot gene expression distribution from overall
                        and cell type-specific perspective
plotPairwiseDistancesDensity
                        Ridgeline Plot of Pairwise Distance Analysis
plotQCvsAnnotation      Scatter plot: QC stats vs Cell Type Annotation
                        Scores
processPCA              Process PCA for SingleCellExperiment Objects
projectPCA              Project Query Data Onto PCA Space of Reference
                        Data
projectSIR              Project Query Data Onto SIR Space of Reference
                        Data
