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

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Documentation for package ‘CAESAR.Suite’ version 0.2.2

• 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