SpatialExperiment
S4 Class for Spatially Resolved -omics Data
Bioconductor version: Release (3.19)
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 | 1.14.0 |
| 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 | ExperimentSubset, SPIAT, alabaster.spatial, imcRtools, tidySpatialExperiment, imcdatasets, MerfishData, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata |
| Imports Me | Banksy, CTSV, DESpace, GSVA, MoleculeExperiment, SpatialFeatureExperiment, SpotClean, SpotSweeper, Statial, VisiumIO, Voyager, cytomapper, escheR, ggspavis, hoodscanR, lisaClust, nnSVG, scider, signifinder, smoothclust, spaSim, spatialDE, spicyR, spoon, stJoincount, standR, tpSVG, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, SpatialDDLS |
| Suggests Me | GeomxTools, SPOTlight, ggsc |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialExperiment_1.14.0.tar.gz |
| Windows Binary (x86_64) | SpatialExperiment_1.14.0.zip |
| macOS Binary (x86_64) | SpatialExperiment_1.14.0.tgz |
| macOS Binary (arm64) | SpatialExperiment_1.14.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |