Function reference • CAESAR.Suite

All functions
`acc()`	Calculate Accuracy of Predicted Cell Types
`add.gene.embedding()`	Add Gene Embedding to Seurat Object
`annotation_mat()`	Annotate Cells Using Distance Matrix and Marker Frequencies
`auc()`	Calculate Area Under the Curve (AUC) for Pathway Scores
`CAESAR.annotation()`	Perform Cell Annotation Using CAESAR with Confidence and Proportion Calculation
`CAESAR.coembedding.image()`	Compute Co-embedding with Image Information Using CAESAR
`CAESAR.coembedding()`	Compute Co-embedding Using CAESAR
`CAESAR.CTDEP()`	Test Cell Type Differentially Enriched Pathways
`CAESAR.enrich.pathway()`	Test whether pathways are enriched
`CAESAR.enrich.score()`	Calculate Spot Level Enrichment Scores for Pathways Using CAESAR
`CAESAR.RUV()`	Perform Batch Correction and Integration with CAESAR Using Housekeeping Genes
`Cauchy.Combination()`	Combine p-values Using the Cauchy Combination Method
`cellembedding_image_matrix()`	Compute Spatial-Aware Cell Embeddings with Image Information
`cellembedding_image_seurat()`	Compute Spatial-Aware Cell Embeddings with Image Information
`cellembedding_matrix()`	Compute Spatial-Aware Cell Embeddings
`cellembedding_seurat()`	Perform CAESAR embedding of Cells Using FAST with Spatial Weights
`CoUMAP.plot()`	Plot Co-embedding UMAP for Genes and Cells
`CoUMAP()`	Co-embedding UMAP for Genes and Cells in a Seurat Object
`find.sig.genes()`	Identify Signature Genes for Each Cell Type
`getneighborhood_fastcpp()`	getneighborhood_fast
`Human_HK_genes`	Human housekeeping genes database
`Intsg()`	Integrate Signature Genes Across Datasets
`marker.select()`	Select Marker Genes from a signature gene list Based on Expression Proportion and Overlap Criteria
`markerList2mat()`	Convert Marker List to a Weighted Matrix
`Mouse_HK_genes`	Mouse housekeeping genes database
`SigScore()`	Calculate Signature Score for Cell Clusters
`toydata`	A toy dataset to run examples

Reference

All functions