SpatialExperiment
S4 Class for Spatially Resolved -omics Data
Bioconductor version: Release (3.20)
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.
Author: Dario Righelli [aut, cre], Davide Risso [aut], Helena L. Crowell [aut], Lukas M. Weber [aut], Nicholas J. Eagles [ctb]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
citation("SpatialExperiment")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")
Introduction to the SpatialExperiment class | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
Version | 1.16.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
License | GPL-3 |
Depends | methods, SingleCellExperiment |
Imports | rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache |
System Requirements | |
URL | https://github.com/drighelli/SpatialExperiment |
Bug Reports | https://github.com/drighelli/SpatialExperiment/issues |
See More
Suggests | knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils |
Linking To | |
Enhances | |
Depends On Me | alabaster.spatial, ExperimentSubset, imcRtools, SPIAT, tidySpatialExperiment, imcdatasets, MerfishData, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata |
Imports Me | Banksy, CatsCradle, concordexR, CTSV, cytomapper, DESpace, escheR, FLAMES, ggspavis, GSVA, hoodscanR, lisaClust, MoleculeExperiment, nnSVG, scider, smoothclust, SpaNorm, spaSim, spatialDE, SpatialFeatureExperiment, spatialSimGP, spicyR, spoon, SpotClean, standR, Statial, stJoincount, tpSVG, VisiumIO, Voyager, xenLite, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, SpatialDDLS |
Suggests Me | GeomxTools, ggsc, SPOTlight |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | SpatialExperiment_1.16.0.tar.gz |
Windows Binary (x86_64) | SpatialExperiment_1.16.0.zip |
macOS Binary (x86_64) | SpatialExperiment_1.16.0.tgz |
macOS Binary (arm64) | SpatialExperiment_1.15.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/SpatialExperiment |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialExperiment |
Bioc Package Browser | https://code.bioconductor.org/browse/SpatialExperiment/ |
Package Short Url | https://bioconductor.org/packages/SpatialExperiment/ |
Package Downloads Report | Download Stats |