SpatialDatasets
This is the released version of SpatialDatasets; for the devel version, see SpatialDatasets.
Collection of spatial omics datasets
Bioconductor version: Release (3.23)
This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.
Author: Farhan Ameen [aut], Nick Robertson [aut], Alex Qin [aut], Shreya Rao [aut], Elijah Willie [aut], Ellis Patrick [aut, cre]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("SpatialDatasets")):
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")
BiocManager::install("SpatialDatasets")
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("SpatialDatasets")| The SpatialDataset package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data, ReproducibleResearch, SingleCellData, SpatialData |
| Version | 1.10.0 |
| License | GPL-3 |
| Depends | ExperimentHub, SpatialExperiment |
| Imports | utils |
| System Requirements | |
| URL | https://github.com/SydneyBioX/SpatialDatasets |
| Bug Reports | https://github.com/SydneyBioX/SpatialDatasets/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, cytomapper |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | lisaClust, spicyR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialDatasets_1.10.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialDatasets |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialDatasets |
| Package Short Url | https://bioconductor.org/packages/SpatialDatasets/ |
| Package Downloads Report | Download Stats |