SpatialExperiment
This is the development version of SpatialExperiment; for the stable release version, see SpatialExperiment.
S4 Class for Spatially Resolved -omics Data
Bioconductor version: Development (3.23)
Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.
Author: Dario Righelli [aut, cre]
, Davide Risso [aut]
, Helena L. Crowell [aut]
, Lukas M. Weber [aut]
, Nicholas J. Eagles [ctb]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
citation("SpatialExperiment")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("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
| Reference Manual |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| License | GPL-3 |
| Depends | methods, SingleCellExperiment |
| Imports | rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache |
| System Requirements | |
| URL | https://github.com/drighelli/SpatialExperiment |
| Bug Reports | https://github.com/drighelli/SpatialExperiment/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |