SpatialExperiment

DOI: 10.18129/B9.bioc.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>

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")

 

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

Details

biocViews	DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	GPL-3
Depends	methods, SingleCellExperiment
Imports	BiocFileCache, DropletUtils, rjson, magick, grDevices, S4Vectors, SummarizedExperiment, BiocGenerics, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
SystemRequirements
Enhances
URL
BugReports	https://github.com/drighelli/SpatialExperiment/issues
Depends On Me	ExperimentSubset, imcRtools, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData
Imports Me	ggspavis, SingleCellMultiModal, spatialDE
Suggests Me	mistyR
Links To Me
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
Package Short Url	https://bioconductor.org/packages/SpatialExperiment/
Package Downloads Report	Download Stats