Spatial analysis of in situ cytometry data
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Documentation for package ‘spicyR’ version 1.12.2
Help Pages
| Accessors | Accessors for SegmentedCells |
| as.data.frame.SegmentedCells | as.data.frame |
| cellAnnotation | Accessors for SegmentedCells |
| cellAnnotation-method | Accessors for SegmentedCells |
| cellAnnotation<- | Accessors for SegmentedCells |
| cellAnnotation<--method | Accessors for SegmentedCells |
| cellID | Accessors for SegmentedCells |
| cellID-method | Accessors for SegmentedCells |
| cellID<- | Accessors for SegmentedCells |
| cellID<--method | Accessors for SegmentedCells |
| cellMarks | Accessors for SegmentedCells |
| cellMarks-method | Accessors for SegmentedCells |
| cellMarks<- | Accessors for SegmentedCells |
| cellMarks<--method | Accessors for SegmentedCells |
| cellMorph | Accessors for SegmentedCells |
| cellMorph-method | Accessors for SegmentedCells |
| cellMorph<- | Accessors for SegmentedCells |
| cellMorph<--method | Accessors for SegmentedCells |
| cellSummary | Accessors for SegmentedCells |
| cellSummary-method | Accessors for SegmentedCells |
| cellSummary<- | Accessors for SegmentedCells |
| cellSummary<--method | Accessors for SegmentedCells |
| cellType | Accessors for SegmentedCells |
| cellType-method | Accessors for SegmentedCells |
| cellType<- | Accessors for SegmentedCells |
| cellType<--method | Accessors for SegmentedCells |
| colTest | Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data fram |
| diabetesData | Diabetes IMC data |
| diabetesData_SCE | Diabetes IMC data in SCE format. |
| filterCells | Accessors for SegmentedCells |
| filterCells-method | Accessors for SegmentedCells |
| getPairwise | Get statistic from pairwise L curve of a single image. |
| getProp | Get proportions from a SegmentedCells, SingleCellExperiment, SpatialExperiment or data.frame. |
| imageCellID | Accessors for SegmentedCells |
| imageCellID-method | Accessors for SegmentedCells |
| imageCellID<- | Accessors for SegmentedCells |
| imageCellID<--method | Accessors for SegmentedCells |
| imageID | Accessors for SegmentedCells |
| imageID-method | Accessors for SegmentedCells |
| imagePheno | Accessors for SegmentedCells |
| imagePheno-method | Accessors for SegmentedCells |
| imagePheno<- | Accessors for SegmentedCells |
| imagePheno<--method | Accessors for SegmentedCells |
| plot | A basic plot for SegmentedCells object |
| plot,SegmentedCells | A basic plot for SegmentedCells object |
| plot-method | A basic plot for SegmentedCells object |
| SegmentedCells | The SegmentedCells class |
| SegmentedCells-class | The SegmentedCells class |
| SegmentedCells-method | The SegmentedCells class |
| show | Show SegmentedCells |
| show-SegmentedCells | Show SegmentedCells |
| signifPlot | Plots result of signifPlot. |
| spicy | Performs spatial tests on spatial cytometry data. |
| spicy-method | Performs spatial tests on spatial cytometry data. |
| SpicyResults-class | Performs spatial tests on spatial cytometry data. |
| SpicyResults-method | Performs spatial tests on spatial cytometry data. |
| spicyTest | Results from spicy for diabetesData |
| spicyTestBootstrap | Results from spicy with bootstrap for diabetesData |
| topPairs | A table of the significant results from spicy tests |
| topPairs-method | A table of the significant results from spicy tests |