CAESAR.CTDEP            Test Cell Type Differentially Enriched Pathways
CAESAR.RUV              Perform Batch Correction and Integration with
                        CAESAR Using Housekeeping Genes
CAESAR.annotation       Perform Cell Annotation Using CAESAR with
                        Confidence and Proportion Calculation
CAESAR.coembedding      Compute Co-embedding Using CAESAR
CAESAR.coembedding.image
                        Compute Co-embedding with Image Information
                        Using CAESAR
CAESAR.enrich.pathway   Test whether pathways are enriched
CAESAR.enrich.score     Calculate Spot Level Enrichment Scores for
                        Pathways Using CAESAR
Cauchy.Combination      Combine p-values Using the Cauchy Combination
                        Method
CoUMAP                  Co-embedding UMAP for Genes and Cells in a
                        Seurat Object
CoUMAP.plot             Plot Co-embedding UMAP for Genes and Cells
Human_HK_genes          Human housekeeping genes database
Intsg                   Integrate Signature Genes Across Datasets
Mouse_HK_genes          Mouse housekeeping genes database
SigScore                Calculate Signature Score for Cell Clusters
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
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
find.sig.genes          Identify Signature Genes for Each Cell Type
getneighborhood_fastcpp
                        getneighborhood_fast
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
toydata                 A toy dataset to run examples
