Installation | Usage | Notes | Contact | Credits | Documentation | Tutorials

pixelatorR

pixelatorR provides the infrastructure to process, analyze and visualize MPX data for R users.

Note

Visit our package website for more details about installation. Here, you can also access the function documentation and tutorials for advanced users.

Installation

pixelatorR can be installed from GitHub by running the following code from R:

install.packages("remotes")
remotes::install_github("PixelgenTechnologies/pixelatorR")

Installation from source

You can also install pixelatorR from source by cloning the repository.

git clone https://github.com/pixelgentechnologies/pixelatorR.git

Then, in an R session, run:

install.packages("<path to pixelatorR directory>", repos = NULL, type = "source")

Usage

Visit our tutorials for a step-by step guide on MPX data analysis with pixelatorR. For advanced users, we also provide additional tutorials on our package website, which are more directed towards users who are interested in the details of how pixelatorR stores and handles MPX data in R.

Notes

pixelatorR is designed to work with objects types from the SeuratObject R package. For many analytical tasks you will need to have Seurat v5 installed:

install.packages("Seurat")

Contact

For feature requests or bug reports, please use the GitHub issues.

You can also email the development team at developers@pixelgen.com.

Credits

pixelatorR is developed and maintained by the developers at Pixelgen Technologies.

When using pixelatorR in your research, please cite the following publication if you are working with Proximity Network Assay data:

Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, et al.. "Single-Cell Protein Interactomes by the Proximity Network Assay". bioRxiv 2025.06.19.660329; doi: https://doi.org/10.1101/2025.06.19.660329

And for Molecular Pixelation data, please cite:

Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. "Molecular pixelation: spatial proteomics of single cells by sequencing." Nature Methods, May 8, 2024. https://doi.org/10.1038/s41592-024-02268-9.

Main developers:

• Ludvig Larsson (@ludvigla)
• Max Karlsson (@maxkarlsson)
• Vincent van Hoef (@vincent-van-hoef)
• Alvaro Martinez Barrio (@ambarrio)
• Johan Dahlberg (@johandahlberg)

A huge thank you to all code contributors!