# Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

## Documentation for package ‘RegionalST’ version 1.11.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DoGSEA | Perform GSEA analysis for cross-regional DE genes
DrawDotplot | Draw dot plot for GSEA results of cross-regional DE genes
DrawRegionProportion | Draw regional cell type distribution with cell type annotation information
DrawRegionProportion_withProp | Draw regional cell type distribution with cellular proportion information
exampleRes | Example DE output
example_sce | Example single cell experiment for input
FindRegionalCells | Identify regional cells given centers and radiuses
GetCellTypeSpecificDE_withProp | Identify cross-regional cell type-specific differential analysis with proportion
GetCrossRegionalDE_raw | Identify cross-regional differential analysis
GetCrossRegionalDE_withProp | Identify cross-regional differential analysis with proportion
GetOneRadiusEntropy | Computer the entropy for a fixed radius
GetOneRadiusEntropy_withProp | Computer the entropy for a fixed radius with cell type proportion
getProportion | Define an accessor method for Proportion_CARD
ManualSelectCenter | Manually select top ROIs
mySpatialPreprocess | Perform Preprocessing for spatial data (tailored from BayesSpace function)
pathways_hallmark | Hallmark database
pathways_kegg | KEGG database
pathways_reactome | REACTOME database
PlotOneSelectedCenter | Plot one selected ROI
RankCenterByEntropy | Automatically rank ROI centers based on entropy
RankCenterByEntropy_withProp | Automatically rank ROI centers based on entropy with proportions