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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Introduction to the SpatialExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0), 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
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialExperiment_1.23.0.tar.gz |
| Windows Binary (x86_64) | SpatialExperiment_1.23.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpatialExperiment_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | SpatialExperiment_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpatialExperiment/ |
| Package Short Url | https://bioconductor.org/packages/SpatialExperiment/ |
| Package Downloads Report | Download Stats |