Package: SpatialExperiment 1.15.1

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_1.15.1.tar.gz
SpatialExperiment_1.15.1.zip(r-4.5)SpatialExperiment_1.15.1.zip(r-4.4)SpatialExperiment_1.15.1.zip(r-4.3)
SpatialExperiment_1.15.1.tgz(r-4.4-any)SpatialExperiment_1.15.1.tgz(r-4.3-any)
SpatialExperiment_1.15.1.tar.gz(r-4.5-noble)SpatialExperiment_1.15.1.tar.gz(r-4.4-noble)
SpatialExperiment_1.15.1.tgz(r-4.4-emscripten)SpatialExperiment_1.15.1.tgz(r-4.3-emscripten)
SpatialExperiment.pdf |SpatialExperiment.html✨
SpatialExperiment/json (API)
NEWS

# 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-1.15.0(bioc 3.20)SpatialExperiment-1.14.0(bioc 3.19)

bioconductor-package

32 exports 5.06 score 64 dependencies 53 dependents

Last updated 20 days agofrom:528b628481

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 crayon curl DBI dbplyr DelayedArray dplyr fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr purrr R6 Rcpp rjson rlang RSQLite S4Arrays S4Vectors SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

Introduction to the SpatialExperiment class

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

Rendered fromSpatialExperiment.Rmdusingknitr::rmarkdownon Jun 21 2024.

Last update: 2022-11-22
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