# Cell type annotation diagnostics

## Documentation for package ‘scDiagnostics’ version 1.6.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
calculateGeneShifts | Calculate Top Loading Gene Expression Shifts
calculateGraphIntegration | Calculate Graph Community Integration Diagnostics
calculateHotellingPValue | Perform Hotelling's T-squared Test on PCA Scores for Single-cell RNA-seq Data
calculateHVGOverlap | Calculate the Overlap Coefficient for Highly Variable Genes
calculateMMDPValue | Calculate Maximum Mean Discrepancy P-Values for Two-Sample Comparison
calculateSIRSpace | Calculate Sliced Inverse Regression (SIR) Space for Different Cell Types
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.calculateDiscriminantSpaceObject | Project Query Data onto a Unified Discriminant Space of Reference Data
plot.calculateGeneShiftsObject | Calculate Top Loading Gene Expression Shifts
plot.calculateGraphIntegrationObject | Calculate Graph Community Integration Diagnostics
plot.calculateSIRSpaceObject | Calculate Sliced Inverse Regression (SIR) Space for Different Cell Types
plot.comparePCAObject | Compare Principal Components Analysis (PCA) Results
plot.detectAnomalyObject | PCA Anomaly Scores via Isolation Forests with 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
regressPC | Plot Regression Results on Principal Components