# Cell type annotation diagnostics

## Documentation for package ‘scDiagnostics’ version 1.0.0

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

## 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
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
calculateVarImpOverlap | Compare Gene Importance Across Datasets Using Random Forest
calculateWassersteinDistance | Compute Wasserstein Distances Between Query and Reference Datasets
histQCvsAnnotation | Histograms: QC Stats and Annotation Scores Visualization
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
projectPCA | Project Query Data Onto PCA Space of Reference Data
projectSIR | Project Query Data Onto SIR Space of Reference Data