SpatialExperiment

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see SpatialExperiment.

S4 Class for Spatial Experiments handling


Bioconductor version: 3.14

Defines S4 classes for storing data for spatial experiments. Main examples are reported by using seqFISH and 10x-Visium Spatial Gene Expression data. This includes specialized methods for storing, retrieving spatial coordinates, 10x dedicated parameters and their handling.

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 "4.1") 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 PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends methods, SingleCellExperiment
Imports BiocFileCache, DropletUtils, rjson, magick, grDevices, S4Vectors, SummarizedExperiment, BiocGenerics, utils
System Requirements
URL
Bug Reports https://github.com/drighelli/SpatialExperiment/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
Linking To
Enhances
Depends On Me ExperimentSubset, imcRtools, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData
Imports Me ggspavis, SingleCellMultiModal, spatialDE
Suggests Me mistyR
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpatialExperiment_1.4.0.tar.gz
Windows Binary SpatialExperiment_1.4.0.zip
macOS 10.13 (High Sierra) SpatialExperiment_1.4.0.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 3.14 Source Archive