MultiAssaySpatialExperiment
This is the development version of MultiAssaySpatialExperiment; to use it, please install the devel version of Bioconductor.
Multi-Assay Experiment with Spatial Context
Bioconductor version: Development (3.24)
Extends MultiAssayExperiment with spatial context elements (images, labels, points, shapes) for integrative analysis of spatially resolved multi-omics data. Supports coercion to and from SpatialExperiment and SpatialFeatureExperiment.
Author: Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp at gene.com>
citation("MultiAssaySpatialExperiment")):Patrick Aboyoun. MultiAssaySpatialExperiment: Multi-Assay Experiment with Spatial Context. doi:10.18129/B9.bioc.MultiAssaySpatialExperiment, R package version 0.99.12, https://bioconductor.org/packages/MultiAssaySpatialExperiment.
Generated from the package metadata; it may differ from the package's own citation.
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("MultiAssaySpatialExperiment")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("MultiAssaySpatialExperiment")| 5. MultiAssaySpatialExperiment cheatsheet | HTML | R Script |
| 4. Design of MultiAssaySpatialExperiment | HTML | R Script |
| 3. MultiAssaySpatialExperiment use cases | HTML | R Script |
| 2. Working with MultiAssaySpatialExperiment | HTML | R Script |
| 1. Introduction to MultiAssaySpatialExperiment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Software, Spatial |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), methods, MultiAssayExperiment |
| Imports | tools, BiocGenerics, BiocParallel, S4Vectors, MatrixGenerics, SummarizedExperiment, SingleCellExperiment, SpatialExperiment, sf |
| System Requirements | |
| URL | https://github.com/Genentech/MultiAssaySpatialExperiment |
| Bug Reports | https://github.com/Genentech/MultiAssaySpatialExperiment/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, arrow, DropletUtils, jsonlite, sfarrow, terra, ggplot2, Matrix, RBioFormats, SpatialFeatureExperiment, spdep, zellkonverter |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BiocDuckDB |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MultiAssaySpatialExperiment_0.99.12.tar.gz |
| Windows Binary (x86_64) | MultiAssaySpatialExperiment_0.99.12.zip |
| macOS Binary (big-sur-x86_64) | MultiAssaySpatialExperiment_0.99.12.tgz |
| macOS Binary (sonoma-arm64) | MultiAssaySpatialExperiment_0.99.12.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MultiAssaySpatialExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MultiAssaySpatialExperiment |
| Package Short Url | https://bioconductor.org/packages/MultiAssaySpatialExperiment/ |
| Package Downloads Report | Download Stats |