SpatialExperiment

DOI: 10.18129/B9.bioc.SpatialExperiment    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SpatialExperiment.

S4 Class for Spatial Experiments handling

Bioconductor version: 3.12

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]

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	10x-Visum Spatial Data Analysis
HTML	R Script	seqFISH Spatial Data Workflow
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	GPL-3
Depends	R (>= 4.0.0), methods, SingleCellExperiment
Imports	S4Vectors
LinkingTo
Suggests	testthat, knitr, rjson, Matrix
SystemRequirements
Enhances
URL
BugReports	https://github.com/drighelli/SpatialExperiment/issues
Depends On Me
Imports Me	SingleCellMultiModal, spatialLIBD
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SpatialExperiment_1.0.0.tar.gz
Windows Binary	SpatialExperiment_1.0.0.zip
macOS 10.13 (High Sierra)	SpatialExperiment_1.0.0.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