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https://github.com/lmweber/ggspavis
Visualization functions for spatial transcriptomics data in R
https://github.com/lmweber/ggspavis
Last synced: 11 days ago
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Visualization functions for spatial transcriptomics data in R
- Host: GitHub
- URL: https://github.com/lmweber/ggspavis
- Owner: lmweber
- License: mit
- Created: 2020-12-02T19:19:24.000Z (almost 4 years ago)
- Default Branch: devel
- Last Pushed: 2024-04-02T16:52:55.000Z (7 months ago)
- Last Synced: 2024-10-11T20:54:16.806Z (28 days ago)
- Language: R
- Homepage:
- Size: 250 KB
- Stars: 2
- Watchers: 2
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# ggspavis
[](https://github.com/lmweber/ggspavis/actions)
The `ggspavis` package contains visualization functions for spatial transcriptomics data, including functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either [SpatialExperiment](https://bioconductor.org/packages/SpatialExperiment) or [SingleCellExperiment](https://bioconductor.org/packages/SingleCellExperiment) Bioconductor format.
The package is available from [Bioconductor](https://bioconductor.org/packages/ggspavis).
## Installation
The release version of the package can be installed from Bioconductor:
```
install.packages("BiocManager")
BiocManager::install("ggspavis")
```
The latest development version can be installed either from the development version of Bioconductor or from GitHub:
```
remotes::install_github("lmweber/ggspavis")
```
## Tutorial
A vignette containing a tutorial and examples is available from the [Bioconductor](https://bioconductor.org/packages/ggspavis) package page.
## 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.