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

## Documentation for package ‘CAESAR.Suite’ version 0.3.0

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

## Help Pages

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