SpatialExperiment

This is the development version of SpatialExperiment; for the stable release version, see SpatialExperiment.

S4 Class for Spatially Resolved -omics Data

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SpatialExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpatialExperiment")

Details

See More

Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO

Linking To

Enhances

Depends On Me alabaster.spatial, clustSIGNAL, ExperimentSubset, imcRtools, SpaceTrooper, SPIAT, tidySpatialExperiment, visiumStitched, imcdatasets, MerfishData, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata

Imports Me Banksy, BulkSignalR, CARDspa, CatsCradle, concordexR, CTSV, cytomapper, DESpace, escheR, FLAMES, ggspavis, GSVA, hoodscanR, lisaClust, MoleculeExperiment, nnSVG, poem, scider, SEraster, signifinder, smoothclust, sosta, spacexr, SpaNorm, spARI, spaSim, spatialDE, SpatialExperimentIO, spatialFDA, SpatialFeatureExperiment, spatialSimGP, spicyR, spoon, SpotClean, SpotSweeper, standR, Statial, stJoincount, stPipe, SVP, tpSVG, VisiumIO, Voyager, XeniumIO, xenLite, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, SpatialDDLS

Suggests Me GeomxTools, ggsc, SPOTlight, zellkonverter, muSpaData

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.