SpatialExperiment

DOI: 10.18129/B9.bioc.SpatialExperiment    

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

S4 Class for Spatial Experiments handling

Bioconductor version: Development (3.13)

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 [ctb], Lukas M. Weber [ctb]

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 (!requireNamespace("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 seqFISH Spatial Data Workflow
HTML R Script Visium Spatial Data Workflow
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.1.432
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 3.5.0), methods, SingleCellExperiment
Imports BiocFileCache, DropletUtils, rjson, magick, grid, S4Vectors, SummarizedExperiment, BiocGenerics, utils
LinkingTo
Suggests knitr, Matrix, testthat, BiocStyle, BumpyMatrix
SystemRequirements
Enhances
URL
BugReports https://github.com/drighelli/SpatialExperiment/issues
Depends On Me MouseGastrulationData, spatialLIBD
Imports Me SingleCellMultiModal
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SpatialExperiment_1.1.432.tar.gz
Windows Binary SpatialExperiment_1.1.432.zip (32- & 64-bit)
macOS 10.13 (High Sierra) SpatialExperiment_1.1.432.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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