Package: SpatialExperiment 1.23.0

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]

SpatialExperiment_1.23.0.tar.gz
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SpatialExperiment_1.23.0.tgz(r-4.6-any)SpatialExperiment_1.23.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpatialExperiment/json (API)

# Install 'SpatialExperiment' in R:

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

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

On BioConductor:SpatialExperiment-1.23.0(bioc 3.24)SpatialExperiment-1.22.0(bioc 3.23)

datarepresentation dataimport infrastructure immunooncology geneexpression transcriptomics singlecell spatial u24ca289073

12.03 score 74 stars 96 packages 3.6k scripts 32 exports 57 dependencies

Last updated from:3bb71a86f6. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	206
linux-devel-x86_64	NOTE	424
source / vignettes	OK	285
linux-release-x86_64	NOTE	393
macos-release-arm64	NOTE	194
macos-oldrel-arm64	NOTE	152
windows-devel	NOTE	259
windows-release	NOTE	249
windows-oldrel	NOTE	253
wasm-release	OK	198

Exports:addImg colData<-getImg imgData imgData<-imgRaster imgRaster<-imgSource imgSource<-mirrorCoords mirrorImg mirrorObject molecules molecules<-read10xVisium readImgData rmvImg rotateCoords rotateImg rotateObject scaleFactors spatialCoords spatialCoords<-spatialCoordsNames spatialCoordsNames<-spatialData spatialData<-spatialDataNames spatialDataNames<-SpatialExperiment SpatialImage toSpatialExperiment

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli cpp11 curl DBI dbplyr DelayedArray dplyr fastmap filelock generics GenomicRanges glue httr2 IRanges lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R6 rappdirs Rcpp rjson rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

Introduction to the SpatialExperiment class

Rendered fromSpatialExperiment.Rmdusingknitr::rmarkdown

Last update: 2024-06-24
Started: 2021-05-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Methods for handling image-related data	addImg 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 experiment	read10xVisium
Read images & scale factors for 10x Genomics Visium	readImgData
Methods for named assays	molecules molecules,SpatialExperiment-method molecules<- molecules<-,SpatialExperiment-method SpatialExperiment-assays
The SpatialExperiment class	SpatialExperiment SpatialExperiment-class
SpatialExperiment coercion methods	coerce, SingleCellExperiment, SpatialExperiment-coercion SpatialExperiment-method toSpatialExperiment
SpatialExperiment colData	colData colData<- colData<-,SpatialExperiment,DataFrame-method colData<-,SpatialExperiment,NULL-method SpatialExperiment-colData
Combining SpatialExperiment objects	cbind,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 methods	show,SpatialExperiment-method SpatialExperiment-misc
Methods for spatial attributes	mirrorCoords mirrorCoords,SpatialExperiment-method mirrorObject mirrorObject,SpatialExperiment-method rotateCoords rotateCoords,SpatialExperiment-method rotateObject rotateObject,SpatialExperiment-method SpatialExperiment-rotate-mirror
Subsetting SpatialExperiment objects	SpatialExperiment-subset [,SpatialExperiment,ANY,ANY,ANY-method
The 'SpatialImage' class	coerce,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' methods	show,VirtualSpatialImage-method SpatialImage-misc