README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# lems-emt-pdl1-models-figures

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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8114631.svg)](https://doi.org/10.5281/zenodo.8114631)
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Models and code to generate figures for “Tumor-Mediated Immunosuppression and Cytokine Spreading Affects the Relation Between EMT and PD-L1 Status”. Frontiers in Immunology. doi: 10.3389/fimmu.2023.1219669

## Usage

### Models

COPASI and Morpheus models can be found in `models/copasi_models` and `models/morpheus_models`, respectively.

### Figures

Figures are generated reproducibly in R using [`renv`](https://rstudio.github.io/renv/index.html):

1. Download/clone this repository
2. Open the project file (`.Rproj`) in RStudio
3. Run 
    ```{r, eval=F}
renv::restore()
```
    to install R package dependencies.

4. Open `code.Rmd` and choose *Run* > *Run All*. Figures will appear in the `output` folder.

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