Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data

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Documentation for package ‘RegionalST’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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