SuperCellCyto is an extension of the SuperCell R package. Initially developed for scRNAseq data, SuperCell aggregates cells with similar transcriptomic profiles into “supercells” (also known as “metacells” in the scRNAseq literature).
In SuperCellCyto, we’ve tailored the SuperCell package to specifically cater to cytometry data:
- Supercells are now aggregating cells that are similar marker expressions.
- Supercells are now created for each individual sample. This adaptation ensures that each supercell encompasses cells from exclusively one sample. By processing each sample independently, we prevent the intermixing of cells from different samples within supercells.
- Multiple samples can now be processed in parallel with a custom load balancing strategy. This enhancement enables simultaneous generation of supercells for multiple samples, significantly reducing the computational time required for processing large datasets.
Vignettes and Function Documentation
Vignettes and function documentations are available on our website: https://phipsonlab.github.io/SuperCellCyto/.
To understand how SuperCellCyto can be integrated into your workflow, head over to the Articles page. Click on the dropdown arrow of the Articles link in the navbar at the top of the website. Our vignettes provide step-by-step guides, practical examples, and use-case scenarios that demonstrate the package’s application in various research contexts.
Documentation and usage of each function in the SuperCellCyto package are available in the Reference page. Click on the Reference link in the navbar at the top of the website.
Citation
If you use SuperCellCyto in your study, please kindly cite our manuscript:
Putri, G.H., Howitt, G., Marsh-Wakefield, F. et al. SuperCellCyto: enabling efficient analysis of large scale cytometry datasets. Genome Biol 25, 89 (2024). https://doi.org/10.1186/s13059-024-03229-3
Installation
The package can be installed using remotes:
# Install remotes
install.packages("remotes")
# Install SuperCellCyto from this repository
remotes::install_github("phipsonlab/SuperCellCyto")SuperCellCyto requires the SuperCell R package installed to run properly. If you use the installation command above, it should be, in theory, automatically installed. But in the case it doesn’t, please manually install it by running the following command beforehand:
# Install SuperCell from their github repository
remotes::install_github("GfellerLab/SuperCell")Code of Conduct
Please note that the SuperCellCyto project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Contribution guide
Please visit Contributing Guide