SpatialExperiment

DOI: 10.18129/B9.bioc.SpatialExperiment  

S4 Class for Spatially Resolved Transcriptomics Data

Bioconductor version: Release (3.16)

Defines an S4 class for storing data from spatially resolved transcriptomics (ST) experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based ST 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]

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction to the SpatialExperiment class
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version	1.8.1
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	methods, SingleCellExperiment
Imports	rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, DropletUtils, BiocGenerics, BiocFileCache
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
SystemRequirements
Enhances
URL	https://github.com/drighelli/SpatialExperiment
BugReports	https://github.com/drighelli/SpatialExperiment/issues
Depends On Me	ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata
Imports Me	CTSV, cytomapper, ggspavis, lisaClust, nnSVG, SingleCellMultiModal, spaSim, spatialDE, SpatialFeatureExperiment, spicyR, SpotClean, standR, stJoincount, Voyager
Suggests Me	GeomxTools, SPOTlight
Links To Me
Build Report

Package Archives

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

Source Package	SpatialExperiment_1.8.1.tar.gz
Windows Binary	SpatialExperiment_1.8.1.zip
macOS Binary (x86_64)	SpatialExperiment_1.8.1.tgz
macOS Binary (arm64)	SpatialExperiment_1.8.1.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
Old Source Packages for BioC 3.16	Source Archive