SpatialExperiment

DOI: 10.18129/B9.bioc.SpatialExperiment    

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

S4 Class for Spatially Resolved Transcriptomics Data

Bioconductor version: Development (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>

Citation (from within R, enter citation("SpatialExperiment")):

Installation

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

 

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 1.7.0
In Bioconductor since BioC 3.12 (R-4.0) (2 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, imcRtools, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData
Imports Me CTSV, ggspavis, lisaClust, nnSVG, SingleCellMultiModal, spaSim, spatialDE, spicyR, SpotClean, standR
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_1.7.0.tar.gz
Windows Binary SpatialExperiment_1.7.0.zip
macOS 10.13 (High Sierra) SpatialExperiment_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpatialExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialExperiment
Package Short Url https://bioconductor.org/packages/SpatialExperiment/
Package Downloads Report Download Stats

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