pixelatorR

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Library for analysis of Molecular Pixelation data in R (Pixelgen Technologies AB)

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# pixelatorR <img src="man/figures/logo.png" align="right" height="138" alt="" />

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

<br/>

> [!NOTE] 
> Visit our [package website](https://pixelgentechnologies.github.io/pixelatorR/) for more details about installation. Here, you can also access the function documentation and tutorials for advanced users.

<br/>

## Installation

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

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

### Installation from source

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

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

Then, in an R session, run:

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

## Usage

Visit our [tutorials](https://software.pixelgen.com/mpx-analysis/introduction) for a step-by step guide on MPX data analysis with pixelatorR. For advanced users, we also provide additional tutorials on our [package website](https://pixelgentechnologies.github.io/pixelatorR/), 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](https://github.com/satijalab/seurat-object) R package. For many analytical tasks you will need to have [Seurat v5](https://satijalab.org/seurat/) installed:

```r
install.packages("Seurat")
```

## Contact

For feature requests or bug reports, please use the GitHub [issues](https://github.com/PixelgenTechnologies/pixelatorR/issues).

You can also email the development team at [developers@pixelgen.com](mailto:developers@pixelgen.com).

## Credits

pixelatorR is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).

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](https://github.com/ludvigla))
- Max Karlsson ([@maxkarlsson](https://github.com/maxkarlsson))
- Vincent van Hoef ([@vincent-van-hoef](https://github.com/vincent-van-hoef))
- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))
- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))

A huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelatorR/graphs/contributors)!

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