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muSpaData

Multi-sample multi-group spatially resolved transcriptomic data

The muSpaData package includes datasets for use in the DESpace package's examples and vignettes. It provides access to a publicly available Stereo-seq spatial dataset with complex experimental designs. This dataset, containing multiple samples (e.g., serial sections) measured under various experimental conditions (e.g., time points), is formatted as SpatialExperiment (SPE) Bioconductor objects. All provided SPEs include processed data and meta data obtained from the original data source.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("muSpaData")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

The development version can be installed from GitHub:

install.packages("remotes")
remotes::install_github("peicai/muSpaData")

Datasets:

  • Wei22_full (SpatialExperiment object):
    A comprehensive spatial transcriptomics dataset at single-cell resolution, capturing axolotl telencephalon regeneration stages. The dataset includes axolotl brain tissues collected from multiple sections across various regeneration stages: 2 (3 sections), 5 (3 sections), 10 (3 sections), 15 (4 sections), and 20 (3 sections) days post injury (DPI). [data source, reference]

  • Wei22_example (SpatialExperiment object): A subset of the Wei22_full dataset, focusing on fewer regeneration stages. This dataset includes 2 DPI (2 sections), 10 DPI (2 sections), and 20 DPI (2 sections) brain tissues.