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 |