scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types belonging to the following six categories.

1. cell type proportions
2. cell type specific gene expressions
3. cell type specific pathway expressions
4. cell type specific cell-cell interaction (CCI) scores
5. overall aggregated gene expressions
6. spatial metrics

Installation

The latest scFeatures can be installed using devtools:

library(devtools)
devtools::install_github("SydneyBioX/scFeatures")

Vignettes

Please see https://sydneybiox.github.io/scFeatures/articles/scFeatures_overview.html.

Reference

Cao, Y., Lin, Y., Patrick, E., Yang, P., & Yang, J. Y. H. (2022). scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. In O. Vitek (Ed.), Bioinformatics (Vol. 38, Issue 20, pp. 4745–4753). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btac590