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

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