This is the computational workflow to analyse physically interacting cells (PICs) in flow cytometry data using R.
Installation
First, please install BPCells. Next, PICtR can be installed using:
install.packages("PICtR", repos = c("https://agshaas.r-universe.dev", "https://cloud.r-project.org"))or directly from GitHub using:
if (!require("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("agSHaas/PICtR")Workflow
Please refer to the Vignette and the Method section of our manuscript for a comprehensive description of the analysis pipeline.
Demo Data
The package comprises a demo data set from LCMV infected mice. Data was analysed using high parametric spectral flow cytometry and can be loaded with data(demo_lcmv). See ?demo_lcmv for details.
Dependencies
The core of this framework relies on Seurat version 5 and BPCells. Please make sure that R is operating in version 4.3 or higher.
Some packages are not necessarily required, but expand the functionality of PICtR. Consider installing:
Citation
If you use PICtR in your work, please cite
Vonficht, Jopp-Saile, Yousefian, Flore et al. Ultra-high-scale cytometry-based cellular interaction mapping. Nature Methods (2025). https://doi.org/10.1038/s41592-025-02744-w