Cell type annotation diagnostics

---

Documentation for package ‘scDiagnostics’ version 1.4.0

• 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
calculateDiscriminantSpace	Project Query Data onto a Unified Discriminant Space of Reference Data
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
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.calculateDiscriminantSpaceObject	Project Query Data onto a Unified Discriminant Space of Reference Data
plot.calculateGraphIntegrationObject	Calculate Graph Community Integration Diagnostics
plot.calculateSIRSpaceObject	Calculate Sliced Inverse Regression (SIR) Space for Different Cell Types
plot.calculateTopLoadingGeneShiftsObject	Calculate Top Loading Gene Expression Shifts
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