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

Need some help? Ask on the Bioconductor Support site!

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

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