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 |