S4 Class for Spatially Resolved -omics Data

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Documentation for package ‘SpatialExperiment’ version 1.19.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

$-method	Methods for spatial attributes
addImg	Methods for handling image-related data
addImg-method	Methods for handling image-related data
cbind-method	Combining SpatialExperiment objects
coerce,	SpatialExperiment coercion methods
coerce-method	The 'SpatialImage' class
colData	SpatialExperiment colData
colData<-	SpatialExperiment colData
colData<--method	SpatialExperiment colData
dim-method	The 'SpatialImage' class
getImg	Methods for handling image-related data
getImg-method	Methods for handling image-related data
imgData	Methods for spatial attributes
imgData-method	Methods for spatial attributes
imgData-methods	Methods for handling image-related data
imgData<-	Methods for spatial attributes
imgData<--method	Methods for spatial attributes
imgRaster	The 'SpatialImage' class
imgRaster-method	The 'SpatialImage' class
imgRaster-method	Methods for handling image-related data
imgRaster<-	The 'SpatialImage' class
imgRaster<--method	The 'SpatialImage' class
imgSource	The 'SpatialImage' class
imgSource-method	The 'SpatialImage' class
imgSource-method	Methods for handling image-related data
imgSource<-	The 'SpatialImage' class
imgSource<--method	The 'SpatialImage' class
LoadedSpatialImage-class	The 'SpatialImage' class
mirrorCoords	Methods for spatial attributes
mirrorCoords-method	Methods for spatial attributes
mirrorImg	The 'SpatialImage' class
mirrorImg-method	The 'SpatialImage' class
mirrorImg-method	Methods for handling image-related data
mirrorObject	Methods for spatial attributes
mirrorObject-method	Methods for spatial attributes
molecules	Methods for named assays
molecules-method	Methods for named assays
molecules<-	Methods for named assays
molecules<--method	Methods for named assays
read10xVisium	Load data from a 10x Genomics Visium experiment
readImgData	Read images & scale factors for 10x Genomics Visium
RemoteSpatialImage-class	The 'SpatialImage' class
rmvImg	Methods for handling image-related data
rmvImg-method	Methods for handling image-related data
rotateCoords	Methods for spatial attributes
rotateCoords-method	Methods for spatial attributes
rotateImg	The 'SpatialImage' class
rotateImg-method	The 'SpatialImage' class
rotateImg-method	Methods for handling image-related data
rotateObject	Methods for spatial attributes
rotateObject-method	Methods for spatial attributes
scaleFactors	Methods for spatial attributes
scaleFactors-method	Methods for spatial attributes
show-method	Miscellaneous SpatialExperiment methods
show-method	Miscellaneous 'SpatialImage' methods
SingleCellExperiment,	SpatialExperiment coercion methods
spatialCoords	Methods for spatial attributes
spatialCoords-method	Methods for spatial attributes
spatialCoords<-	Methods for spatial attributes
spatialCoords<--method	Methods for spatial attributes
spatialCoordsNames	Methods for spatial attributes
spatialCoordsNames-method	Methods for spatial attributes
spatialCoordsNames<-	Methods for spatial attributes
spatialCoordsNames<--method	Methods for spatial attributes
spatialData	Methods for spatial attributes
spatialData-method	Methods for spatial attributes
spatialData<-	Methods for spatial attributes
spatialData<--method	Methods for spatial attributes
spatialDataNames	Methods for spatial attributes
spatialDataNames-method	Methods for spatial attributes
spatialDataNames<-	Methods for spatial attributes
spatialDataNames<--method	Methods for spatial attributes
SpatialExperiment	The SpatialExperiment class
SpatialExperiment-assays	Methods for named assays
SpatialExperiment-class	The SpatialExperiment class
SpatialExperiment-coercion	SpatialExperiment coercion methods
SpatialExperiment-colData	SpatialExperiment colData
SpatialExperiment-combine	Combining SpatialExperiment objects
SpatialExperiment-method	SpatialExperiment coercion methods
SpatialExperiment-methods	Methods for spatial attributes
SpatialExperiment-misc	Miscellaneous SpatialExperiment methods
SpatialExperiment-rotate-mirror	Methods for spatial attributes
SpatialExperiment-subset	Subsetting SpatialExperiment objects
SpatialImage	The 'SpatialImage' class
SpatialImage-class	The 'SpatialImage' class
SpatialImage-misc	Miscellaneous 'SpatialImage' methods
StoredSpatialImage-class	The 'SpatialImage' class
toSpatialExperiment	SpatialExperiment coercion methods
VirtualSpatialImage-class	The 'SpatialImage' class
[-method	Subsetting SpatialExperiment objects