SpatialData.data
This is the development version of SpatialData.data; to use it, please install the devel version of Bioconductor.
SpatialData datasets
Bioconductor version: Development (3.24)
A companion package to access scverse-curated example SpatialData stores. The datasets span spatial omics technologies such as Visium, Visium HD, Xenium, MERFISH, MIBI-TOF, and imaging mass cytometry, and are distributed as zipped Zarr stores through the Bioconductor bucket on the NSF Open Storage Network (OSN) or the scverse spatialdata sandbox. Available datasets and their metadata can be listed, and each dataset is downloaded once, cached locally with 'BiocFileCache', and read into R as a SpatialData object via 'spatialdataR' package.
Author: Helena L. Crowell [aut, cre]
, Artür Manukyan [aut]
, Hugo Gruson [aut]
, Vince Carey [aut]
Maintainer: Helena L. Crowell <helena at crowell.eu>
citation("SpatialData.data")):
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("SpatialData.data")
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("SpatialData.data")| SpatialData.data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.10 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | utils, BiocFileCache, spatialdataR, paws.storage |
| System Requirements | |
| URL | https://github.com/HelenaLC/SpatialData.data https://helenalc.github.io/SpatialData.data/ |
| Bug Reports | https://github.com/HelenaLC/SpatialData.data/issues |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialData.data_0.99.10.tar.gz |
| Windows Binary (x86_64) | SpatialData.data_0.99.10.zip |
| macOS Binary (big-sur-x86_64) | SpatialData.data_0.99.10.tgz |
| macOS Binary (sonoma-arm64) | SpatialData.data_0.99.10.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialData.data |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialData.data |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpatialData.data/ |
| Package Short Url | https://bioconductor.org/packages/SpatialData.data/ |
| Package Downloads Report | Download Stats |