https://github.com/bioconductor-source/spatialexperiment
Science Score: 26.0%
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Low similarity (11.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 1.98 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
SpatialExperiment
SpatialExperiment is an R/Bioconductor S4 class for storing data from spatial -omics experiments. The class extends the SingleCellExperiment class for single-cell data 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.
The SpatialExperiment package is available from Bioconductor.
A vignette containing examples and documentation is available from Bioconductor, and additional details are provided in our paper.
The following schematic illustrates the SpatialExperiment class structure.
Installation
The current release version of the SpatialExperiment package can be installed from Bioconductor as follows. This is the recommended approach for most users.
install.packages("BiocManager")
BiocManager::install("SpatialExperiment")
The latest development version can be installed from the development version of Bioconductor or from GitHub (which may also require some dependency packages to be installed manually).
remotes::install_github("drighelli/SpatialExperiment")
Citation
Righell D.*, Weber L.M.*, Crowell H.L.*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.+, and Risso D.+ (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11), 3128-3131.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- docker/build-push-action v4 composite
- docker/login-action v2 composite
- docker/setup-buildx-action v2 composite
- docker/setup-qemu-action v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- SingleCellExperiment * depends
- methods * depends
- BiocFileCache * imports
- BiocGenerics * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- grDevices * imports
- magick * imports
- rjson * imports
- utils * imports
- BiocStyle * suggests
- BumpyMatrix * suggests
- DropletUtils * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests