Reference

Visualization of Cell Type Annotations
boxplotPCA()	Plot Principal Components for Different Cell Types
calculateDiscriminantSpace() plot(<calculateDiscriminantSpaceObject>)	Project Query Data onto Discriminant Space of Reference Data
calculateSIRSpace() plot(<calculateSIRSpaceObject>)	Calculate Sliced Inverse Regression (SIR) Space for Different Cell Types
plotCellTypeMDS()	Plot Reference and Query Cell Types using MDS
plotCellTypePCA()	Plot Principal Components for Different Cell Types
Visualization of Marker Expressions
plotGeneExpressionDimred()	Visualize gene expression on a dimensional reduction plot
plotMarkerExpression()	Plot gene expression distribution from overall and cell type-specific perspective
Visualization of QC and Annotation Scores
histQCvsAnnotation()	Histograms: QC Stats and Annotation Scores Visualization
plotQCvsAnnotation()	Scatter plot: QC stats vs Cell Type Annotation Scores
plotGeneSetScores()	Visualization of gene sets or pathway scores on dimensional reduction plot
Evaluation of Dataset Alignment
compareCCA() plot(<compareCCAObject>)	Compare Canonical Correlation Analysis (CCA) between Query and Reference Data
comparePCA() plot(<comparePCAObject>)	Compare Principal Components Analysis (PCA) Results
comparePCASubspace() plot(<comparePCASubspaceObject>)	Compare Subspaces Spanned by Top Principal Components
plotPairwiseDistancesDensity()	Pairwise Distance Analysis and Density Visualization
plotWassersteinDistance()	Density Plot of Wasserstein Distances Under Null Distribution
Evaluation of Marker Gene Alignment
calculateHVGOverlap()	Calculate the Overlap Coefficient for Highly Variable Genes
calculateVarImpOverlap()	Compare Gene Importance Across Datasets Using Random Forest
Calculation of Statistical Measures to Compare Two Datasets
calculateCramerPValue()	Calculate Cramer Test P-Values for Two-Sample Comparison of Multivariate ECDFs
calculateHotellingPValue()	Perform Hotelling's T-squared Test on PCA Scores for Single-cell RNA-seq Data
calculateNearestNeighborProbabilities() plot(<calculateNearestNeighborProbabilitiesObject>)	Calculate Nearest Neighbor Diagnostics for Cell Type Classification
calculateAveragePairwiseCorrelation() plot(<calculateAveragePairwiseCorrelationObject>)	Compute Average Pairwise Correlation between Cell Types
plot(<regressPCObject>) regressPC()	Plot Regression Results on Principal Components
Anomaly Detection (Global and Cell Type-Specific)
detectAnomaly() plot(<detectAnomalyObject>)	PCA Anomaly Scores via Isolation Forests with Visualization
calculateCellSimilarityPCA() plot(<calculateCellSimilarityPCAObject>)	Calculate Cell Similarity Using PCA Loadings
Calculation of Distances Between Specific Cells and Cell Populations
calculateCellDistances() plot(<calculateCellDistancesObject>)	Compute Cell Distances Between Reference and Query Data
calculateCellDistancesSimilarity()	Function to Calculate Bhattacharyya Coefficients and Hellinger Distances
Misc
projectPCA()	Project Query Data Onto PCA Space of Reference Data
projectSIR()	Project Query Data Onto SIR Space of Reference Data
calculateCategorizationEntropy()	Calculate Categorization Entropy
Datasets
reference_data	Reference Single-Cell RNA-Seq Dataset
query_data	Query Single-Cell RNA-Seq Dataset
qc_data	Quality Control Single-Cell RNA-Seq Dataset