Package 'muSpaData'

Title: Multi-sample multi-group spatially resolved transcriptomic data
Description: Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format.
Authors: Peiying Cai [aut, cre] (ORCID: <https://orcid.org/0009-0001-9229-2244>)
Maintainer: Peiying Cai <[email protected]>
License: MIT + file LICENSE
Version: 1.4.0
Built: 2026-10-10 11:21:05 UTC
Source: https://github.com/bioc/muSpaData

Help Index

Wei22_example dataset

Description

  • A subset of the Wei22_full dataset, focusing on fewer regeneration stages.

  • It includes 2 (2 sections), 10 (2 sections), and 20 (2 sections) days post injury (DPI).

  • The original data is deposited in the Spatial Transcript Omics DataBase (STOmics DB) under dataset id STDS0000056.

Usage

Wei22_example(metadata = FALSE)

Arguments

metadata

A logical value indicating whether to return only the ExperimentHub metadata, which describes the overall dataset, or to load the entire dataset. Defaults to FALSE.

Details

link to reference:

https://www.science.org/doi/10.1126/science.abp9444

link to raw data:

https://db.cngb.org/stomics/artista/download/

Value

an object of class SpatialExperiment.

Author(s)

Peiying Cai [email protected]

References

Wei et al. (2022). "Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration", Science, 377(6610).

Examples

# load metadata only
Wei22_example(metadata = TRUE)

# load SpatialExperiment
Wei22_example(metadata = FALSE)

Wei22_full dataset

Description

  • Single-cell Stereo-seq spatial transcriptomics data includes axolotl brain tissues collected from multiple sections across five regeneration stages (16 samples in total)

  • The dataset contains 13890 features across 147432 cells, and preprocessing has been applied.

  • The original data is deposited in the Spatial Transcript Omics DataBase (STOmics DB) under dataset id STDS0000056.

Usage

Wei22_full(metadata = FALSE)

Arguments

metadata

A logical value indicating whether to return only the ExperimentHub metadata, which describes the overall dataset, or to load the entire dataset. Defaults to FALSE.

Details

link to reference:

https://www.science.org/doi/10.1126/science.abp9444

link to raw data:

https://db.cngb.org/stomics/artista/download/

Value

an object of class SpatialExperiment.

Author(s)

Peiying Cai [email protected]

References

Wei et al. (2022). "Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration", Science, 377(6610).

Examples

# load metadata only
Wei22_full(metadata = TRUE)

# load SpatialExperiment
Wei22_full(metadata = FALSE)