A B C D F I L M N R S T U V misc
| addImg-method | Images in SpatialFeatureExperiment object |
| addVisiumSpotPoly | Add Visium spot polygons to colGeometry |
| annotGeometries | Annotation geometry methods |
| annotGeometries-method | Annotation geometry methods |
| annotGeometries<- | Annotation geometry methods |
| annotGeometries<--method | Annotation geometry methods |
| annotGeometry | Annotation geometry methods |
| annotGeometry-method | Annotation geometry methods |
| annotGeometry<- | Annotation geometry methods |
| annotGeometry<--method | Annotation geometry methods |
| annotGeometryNames | Annotation geometry methods |
| annotGeometryNames-method | Annotation geometry methods |
| annotGeometryNames<- | Annotation geometry methods |
| annotGeometryNames<--method | Annotation geometry methods |
| annotGraph | Spatial graph methods |
| annotGraph<- | Spatial graph methods |
| annotGraphNames | Spatial graph methods |
| annotGraphNames<- | Spatial graph methods |
| annotGraphs | Spatial graph methods |
| annotGraphs-method | Spatial graph methods |
| annotGraphs<- | Spatial graph methods |
| annotGraphs<--method | Spatial graph methods |
| annotNPred | Binary predicates for geometry of each cell/spot and annotation |
| annotOp | Binary operations for geometry of each cell/spot and annotation |
| annotPred | Binary predicates for geometry of each cell/spot and annotation |
| annotSummary | Summarize attributes of an annotGeometry for each cell/spot |
| bbox | Find bounding box of SFE objects |
| bbox-method | Find bounding box of SFE objects |
| cbind-method | Concatenate SpatialFeatureExperiment objects |
| cellSeg | Dimension geometry methods |
| cellSeg<- | Dimension geometry methods |
| centroids | Dimension geometry methods |
| centroids<- | Dimension geometry methods |
| changeSampleIDs | Change sample IDs |
| colGeometries | Dimension geometry methods |
| colGeometries<- | Dimension geometry methods |
| colGeometry | Dimension geometry methods |
| colGeometry<- | Dimension geometry methods |
| colGeometryNames | Dimension geometry methods |
| colGeometryNames<- | Dimension geometry methods |
| colGraph | Spatial graph methods |
| colGraph<- | Spatial graph methods |
| colGraphNames | Spatial graph methods |
| colGraphNames<- | Spatial graph methods |
| colGraphs | Spatial graph methods |
| colGraphs-method | Spatial graph methods |
| colGraphs<- | Spatial graph methods |
| colGraphs<--method | Spatial graph methods |
| crop | Crop an SFE object with a geometry |
| df2sf | From ordinary data frame to sf to construct SFE object |
| dimGeometries | Dimension geometry methods |
| dimGeometries-method | Dimension geometry methods |
| dimGeometries<- | Dimension geometry methods |
| dimGeometries<--method | Dimension geometry methods |
| dimGeometry | Dimension geometry methods |
| dimGeometry-method | Dimension geometry methods |
| dimGeometry<- | Dimension geometry methods |
| dimGeometry<--method | Dimension geometry methods |
| dimGeometryNames | Dimension geometry methods |
| dimGeometryNames-method | Dimension geometry methods |
| dimGeometryNames<- | Dimension geometry methods |
| dimGeometryNames<--method | Dimension geometry methods |
| findSpatialNeighbors | Find spatial neighborhood graph |
| findSpatialNeighbors-method | Find spatial neighborhood graph |
| findVisiumGraph | Find spatial neighborhood graphs for Visium spots |
| imgRaster-method | Images in SpatialFeatureExperiment object |
| imgSource-method | Images in SpatialFeatureExperiment object |
| localResult | Organize results from local spatial statistics |
| localResult-method | Organize results from local spatial statistics |
| localResult<- | Organize results from local spatial statistics |
| localResult<--method | Organize results from local spatial statistics |
| localResultAttrs | Organize results from local spatial statistics |
| localResultAttrs-method | Organize results from local spatial statistics |
| localResultFeatures | Organize results from local spatial statistics |
| localResultFeatures-method | Organize results from local spatial statistics |
| localResultNames | Organize results from local spatial statistics |
| localResultNames-method | Organize results from local spatial statistics |
| localResultNames<- | Organize results from local spatial statistics |
| localResultNames<--method | Organize results from local spatial statistics |
| localResults | Organize results from local spatial statistics |
| localResults-method | Organize results from local spatial statistics |
| localResults<- | Organize results from local spatial statistics |
| localResults<--method | Organize results from local spatial statistics |
| mirror | Transpose or mirror SFE object in histological space |
| mirrorImg-method | Images in SpatialFeatureExperiment object |
| nucSeg | Dimension geometry methods |
| nucSeg<- | Dimension geometry methods |
| read10xVisiumSFE | Read 10X Visium data as SpatialFeatureExperiment |
| readVizgen | Read Vizgen MERFISH output as SpatialFeatureExperiment |
| removeEmptySpace | Remove empty space |
| ROIPoly | Dimension geometry methods |
| ROIPoly<- | Dimension geometry methods |
| rowGeometries | Dimension geometry methods |
| rowGeometries<- | Dimension geometry methods |
| rowGeometry | Dimension geometry methods |
| rowGeometry<- | Dimension geometry methods |
| rowGeometryNames | Dimension geometry methods |
| rowGeometryNames<- | Dimension geometry methods |
| rowGraph | Spatial graph methods |
| rowGraph<- | Spatial graph methods |
| rowGraphNames | Spatial graph methods |
| rowGraphNames<- | Spatial graph methods |
| rowGraphs | Spatial graph methods |
| rowGraphs-method | Spatial graph methods |
| rowGraphs<- | Spatial graph methods |
| rowGraphs<--method | Spatial graph methods |
| sampleIDs | Get all unique sample IDs |
| saveRDS-method | Save SpatialFeatureExperiment as RDS file |
| SFE-image | Images in SpatialFeatureExperiment object |
| SFE-transform | Transpose or mirror SFE object in histological space |
| SFEVersion | Update a SpatialFeatureExperiment object |
| show-method | Print method for SpatialFeatureExperiment |
| SpatialFeatureExperiment | Constructor of SpatialFeatureExperiment object |
| SpatialFeatureExperiment-class | The SpatialFeatureExperiment class |
| SpatialFeatureExperiment-coercion | SpatialFeatureExperiment coercion methods |
| SpatialFeatureExperiment-subset | Subsetting SpatialFeatureExperiment objects |
| spatialGraph | Spatial graph methods |
| spatialGraph-method | Spatial graph methods |
| spatialGraph<- | Spatial graph methods |
| spatialGraph<--method | Spatial graph methods |
| spatialGraphNames | Spatial graph methods |
| spatialGraphNames-method | Spatial graph methods |
| spatialGraphNames<- | Spatial graph methods |
| spatialGraphNames<--method | Spatial graph methods |
| spatialGraphs | Spatial graph methods |
| spatialGraphs-method | Spatial graph methods |
| spatialGraphs<- | Spatial graph methods |
| spatialGraphs<--method | Spatial graph methods |
| SpatRasterImage-class | Images in SpatialFeatureExperiment object |
| spotPoly | Dimension geometry methods |
| spotPoly<- | Dimension geometry methods |
| st_any_intersects | Simple geometry predicates |
| st_any_pred | Simple geometry predicates |
| st_n_intersects | Simple geometry predicates |
| st_n_pred | Simple geometry predicates |
| tissueBoundary | Annotation geometry methods |
| tissueBoundary<- | Annotation geometry methods |
| toSpatialFeatureExperiment | SpatialFeatureExperiment coercion methods |
| toSpatialFeatureExperiment-method | SpatialFeatureExperiment coercion methods |
| transpose | Transpose or mirror SFE object in histological space |
| transposeImg | Images in SpatialFeatureExperiment object |
| transposeImg-method | Images in SpatialFeatureExperiment object |
| txSpots | Dimension geometry methods |
| txSpots<- | Dimension geometry methods |
| unit | Get unit of a SpatialFeatureExperiment |
| unit-method | Get unit of a SpatialFeatureExperiment |
| updateObject | Update a SpatialFeatureExperiment object |
| updateObject-method | Update a SpatialFeatureExperiment object |
| visium_row_col | Row and columns of Visium barcodes on the slide |
| [-method | Subsetting SpatialFeatureExperiment objects |