Man pages for pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf
| addVisiumSpotPoly | Add Visium spot polygons to colGeometry |
| annotGeometries | Annotation geometry methods |
| annotOp | Binary operations for geometry of each cell/spot and... |
| annotPred | Binary predicates for geometry of each cell/spot and... |
| annotSummary | Summarize attributes of an annotGeometry for each cell/spot |
| bbox-SpatialFeatureExperiment-method | Find bounding box of SFE objects |
| cbind-SpatialFeatureExperiment-method | Concatenate SpatialFeatureExperiment objects |
| changeSampleIDs | Change sample IDs |
| crop | Crop an SFE object with a geometry |
| df2sf | From ordinary data frame to sf to construct SFE object |
| dimGeometries | Dimension geometry methods |
| findSpatialNeighbors-SpatialFeatureExperiment-method | Find spatial neighborhood graph |
| findVisiumGraph | Find spatial neighborhood graphs for Visium spots |
| internal-Voyager | Internal functions also used in Voyager |
| localResults | Organize results from local spatial statistics |
| read10xVisiumSFE | Read 10X Visium data as SpatialFeatureExperiment |
| readVizgen | Read Vizgen MERFISH output as SpatialFeatureExperiment |
| reexports | Objects exported from other packages |
| removeEmptySpace | Remove empty space |
| sampleIDs | Get all unique sample IDs |
| saveRDS-SpatialFeatureExperiment-method | Save SpatialFeatureExperiment as RDS file |
| SFE-image | Images in SpatialFeatureExperiment object |
| SFE-transform | Transpose or mirror SFE object in histological space |
| show-SpatialFeatureExperiment-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 |
| spatialGraphs | Spatial graph methods |
| st_any_pred | Simple geometry predicates |
| unit-SpatialFeatureExperiment-method | Get unit of a SpatialFeatureExperiment |
| updateObject | Update a SpatialFeatureExperiment object |
| visium_row_col | Row and columns of Visium barcodes on the slide |
