SpatialExperiment

DOI: 10.18129/B9.bioc.SpatialExperiment    

S4 Class for Spatial Experiments handling

Bioconductor version: Release (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>

Citation (from within R, enter citation("SpatialExperiment")):

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) (< 6 months)
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

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