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("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 | ||
| NEWS | Text |
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 |
See More
| 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 [email protected]: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 |