Package: SpatialExperiment 1.17.0

Dario Righelli

SpatialExperiment: S4 Class for Spatially Resolved -omics Data

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

Authors:Dario Righelli [aut, cre], Davide Risso [aut], Helena L. Crowell [aut], Lukas M. Weber [aut], Nicholas J. Eagles [ctb]

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SpatialExperiment/json (API)
NEWS

# Install 'SpatialExperiment' in R:
install.packages('SpatialExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/drighelli/spatialexperiment/issues

On BioConductor:SpatialExperiment-1.17.0(bioc 3.21)SpatialExperiment-1.16.0(bioc 3.20)

datarepresentationdataimportinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial

12.44 score 56 stars 63 packages 1.3k scripts 6.9k downloads 32 exports 64 dependencies

Last updated 2 months agofrom:29a659f6df. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-winNOTEDec 14 2024
R-4.5-linuxNOTEDec 14 2024
R-4.4-winNOTEDec 14 2024
R-4.4-macNOTEDec 14 2024
R-4.3-winNOTEDec 14 2024
R-4.3-macNOTEDec 14 2024

Exports:addImgcolData<-getImgimgDataimgData<-imgRasterimgRaster<-imgSourceimgSource<-mirrorCoordsmirrorImgmirrorObjectmoleculesmolecules<-read10xVisiumreadImgDatarmvImgrotateCoordsrotateImgrotateObjectscaleFactorsspatialCoordsspatialCoords<-spatialCoordsNamesspatialCoordsNames<-spatialDataspatialData<-spatialDataNamesspatialDataNames<-SpatialExperimentSpatialImagetoSpatialExperiment

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR6RcpprjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc

Introduction to the SpatialExperiment class

Dario Righelli, Helena L. Crowell, Lukas M. Weber

Rendered fromSpatialExperiment.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2022-11-22
Started: 2021-05-05

Readme and manuals

Help Manual

Help pageTopics
Methods for handling image-related dataaddImg addImg,SpatialExperiment-method getImg getImg,SpatialExperiment-method imgData-methods imgRaster,SpatialExperiment-method imgSource,SpatialExperiment-method mirrorImg,SpatialExperiment-method rmvImg rmvImg,SpatialExperiment-method rotateImg,SpatialExperiment-method
Load data from a 10x Genomics Visium experimentread10xVisium
Read images & scale factors for 10x Genomics VisiumreadImgData
Methods for named assaysmolecules molecules,SpatialExperiment-method molecules<- molecules<-,SpatialExperiment-method SpatialExperiment-assays
The SpatialExperiment classSpatialExperiment SpatialExperiment-class
SpatialExperiment coercion methodscoerce, SingleCellExperiment, SpatialExperiment-coercion SpatialExperiment-method toSpatialExperiment
SpatialExperiment colDatacolData colData<- colData<-,SpatialExperiment,DataFrame-method colData<-,SpatialExperiment,NULL-method SpatialExperiment-colData
Combining SpatialExperiment objectscbind,SingleCellExperiment-method cbind,SpatialExperiment-method SpatialExperiment-combine
Methods for spatial attributes$,SpatialExperiment-method imgData imgData,SpatialExperiment-method imgData<- imgData<-,SpatialExperiment,DataFrame-method imgData<-,SpatialExperiment,NULL-method scaleFactors scaleFactors,SpatialExperiment-method spatialCoords spatialCoords,SpatialExperiment-method spatialCoords<- spatialCoords<-,SpatialExperiment,matrix-method spatialCoords<-,SpatialExperiment,NULL-method spatialCoordsNames spatialCoordsNames,SpatialExperiment-method spatialCoordsNames<- spatialCoordsNames<-,SpatialExperiment,character-method spatialCoordsNames<-,SpatialExperiment,NULL-method spatialData spatialData,SpatialExperiment-method spatialData<- spatialData<-,SpatialExperiment,DFrame-method spatialData<-,SpatialExperiment,NULL-method spatialDataNames spatialDataNames,SpatialExperiment-method spatialDataNames<- spatialDataNames<-,SpatialExperiment,character-method spatialDataNames<-,SpatialExperiment,NULL-method SpatialExperiment-methods
Miscellaneous SpatialExperiment methodsshow,SpatialExperiment-method SpatialExperiment-misc
Methods for spatial attributesmirrorCoords mirrorCoords,SpatialExperiment-method mirrorObject mirrorObject,SpatialExperiment-method rotateCoords rotateCoords,SpatialExperiment-method rotateObject rotateObject,SpatialExperiment-method SpatialExperiment-rotate-mirror
Subsetting SpatialExperiment objectsSpatialExperiment-subset [,SpatialExperiment,ANY,ANY,ANY-method
The 'SpatialImage' classcoerce,RemoteSpatialImage,StoredSpatialImage-method coerce,VirtualSpatialImage,LoadedSpatialImage-method dim,StoredSpatialImage-method dim,VirtualSpatialImage-method imgRaster imgRaster,LoadedSpatialImage-method imgRaster,RemoteSpatialImage-method imgRaster,StoredSpatialImage-method imgRaster<- imgRaster<-,LoadedSpatialImage-method imgSource imgSource,LoadedSpatialImage-method imgSource,RemoteSpatialImage-method imgSource,StoredSpatialImage-method imgSource<- imgSource<-,RemoteSpatialImage,character-method imgSource<-,StoredSpatialImage,character-method LoadedSpatialImage-class mirrorImg mirrorImg,LoadedSpatialImage-method mirrorImg,VirtualSpatialImage-method RemoteSpatialImage-class rotateImg rotateImg,LoadedSpatialImage-method rotateImg,VirtualSpatialImage-method SpatialImage SpatialImage-class StoredSpatialImage-class VirtualSpatialImage-class
Miscellaneous 'SpatialImage' methodsshow,VirtualSpatialImage-method SpatialImage-misc