CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation


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Documentation for package ‘CAESAR.Suite’ version 0.1.0

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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 Compute Co-embedding Using CAESAR
CAESAR.coembedding.image Compute Co-embedding with Image Information 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 Co-embedding UMAP for Genes and Cells in a Seurat Object
CoUMAP.plot Plot Co-embedding UMAP for Genes and Cells
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