SpatialExperiment
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SpatialExperiment.
S4 Class for Spatial Experiments handling
Bioconductor version: 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("SpatialExperiment")):
Installation
To install this package, start R (version "4.0") 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")| 10x-Visum Spatial Data Analysis | HTML | R Script |
| seqFISH Spatial Data Workflow | HTML | R Script |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, ImmunoOncology, Infrastructure, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0), methods, SingleCellExperiment |
| Imports | S4Vectors |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/drighelli/SpatialExperiment/issues |
See More
| Suggests | testthat, knitr, rjson, Matrix |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | SingleCellMultiModal, spatialLIBD |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.12 | Source Archive |