SpatialExperiment
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SpatialExperiment.
S4 Class for Spatially Resolved Transcriptomics Data
Bioconductor version: 3.16
Defines an S4 class for storing data from spatially resolved transcriptomics (ST) experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based ST 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]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
citation("SpatialExperiment")):
Installation
To install this package, start R (version "4.2") 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, Spatial, Transcriptomics |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL-3 |
| Depends | methods, SingleCellExperiment |
| Imports | rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, DropletUtils, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata |
| Imports Me | CTSV, cytomapper, ggspavis, lisaClust, nnSVG, SingleCellMultiModal, spaSim, spatialDE, SpatialFeatureExperiment, spicyR, SpotClean, standR, stJoincount, Voyager |
| Suggests Me | GeomxTools, SPOTlight |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialExperiment_1.8.1.tar.gz |
| Windows Binary | SpatialExperiment_1.8.1.zip |
| macOS Binary (x86_64) | SpatialExperiment_1.8.1.tgz |
| macOS Binary (arm64) | SpatialExperiment_1.8.1.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 |
| Old Source Packages for BioC 3.16 | Source Archive |