Investigating regions of interest and performing regional cell
type-specific analysis with spatial transcriptomics data
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Documentation for package ‘RegionalST’ version 1.5.8
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 |