https://github.com/lmweber/stexampledata

Collection of spatially resolved transcriptomics datasets in SpatialExperiment R/Bioconductor format
https://github.com/lmweber/stexampledata

Last synced: 2 days ago
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Collection of spatially resolved transcriptomics datasets in SpatialExperiment R/Bioconductor format

• Host: GitHub
• URL: https://github.com/lmweber/stexampledata
• Owner: lmweber
• License: mit
• Created: 2020-06-24T21:43:44.000Z (over 4 years ago)
• Default Branch: devel
• Last Pushed: 2024-05-17T16:31:27.000Z (6 months ago)
• Last Synced: 2024-10-11T22:26:36.142Z (28 days ago)
• Language: R
• Homepage:
• Size: 187 KB
• Stars: 1
• Watchers: 2
• Forks: 4
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# STexampleData

[![R build status](https://github.com/lmweber/STexampleData/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/lmweber/STexampleData/actions)

The `STexampleData` package contains a collection of spatial transcriptomics datasets, which have been formatted into the [SpatialExperiment](https://bioconductor.org/packages/SpatialExperiment) Bioconductor class, for use in examples, demonstrations, and tutorials. The datasets are from several different technological platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels.

The `STexampleData` package is available from [Bioconductor](https://bioconductor.org/packages/STexampleData).

A vignette containing examples and documentation is available from [Bioconductor](https://bioconductor.org/packages/STexampleData).

## Installation

The release version of the `STexampleData` package can be installed from Bioconductor:

```

install.packages("BiocManager")

BiocManager::install("STexampleData")

```

The development version can be installed from the development version of Bioconductor (see Bioconductor website for details) or from GitHub:

```

install.packages("remotes")

remotes::install_github("lmweber/STexampleData")

```

## 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](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac299/6575443), btac299.