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 = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# `CroCoNet` <img src="man/figures/logo.png" align="right" width="17.5%" /> <br/>  Cro<span style="font-weight:normal">ss-species</span> <br/> Co<span style="font-weight:normal">mparison of</span> <br/> Net<span style="font-weight:normal">works</span>

CroCoNet is a framework to quantitatively compare gene regulatory networks across species and identify conserved and diverged modules. It hinges on contrasting module variability within and across species in order to distinguish true evolutionary divergence from confounding factors such as diversity across individuals, environmental differences and technical noise.

<p align="center">
  <img src="man/figures/pipeline.png" alt="Pipeline" width="100%" />
  <br>
  <sup>The main steps of the CroCoNet workflow</sup>
</p>

## :arrow_down: Installation

For the installation, the R package `devtools` is needed.

```{r, echo=T, eval=F, tidy=T}
install.packages('devtools')
library(devtools)
```

Once `devtools` is available, you can install the development version of `CroCoNet` and all its dependencies from GitHub with:

``` {r, echo=T, eval=F, tidy=T}
devtools::install_github("Hellmann-Lab/CroCoNet")
```

## :book: User guide

For a step-by-step guide and detailed explanations, please check out the vignette on the analysis of an example scRNA-seq dataset:

```{r, echo=T, eval=F, tidy=T}
browseVignettes('CroCoNet')
```

You can access this vignette, along with the documentation of all functions, on the [CroCoNet website](hellmann-lab.github.io/CroCoNet/) as well.

## :scroll: Citation

The CroCoNet framework and its biological applications are described in detail in our [preprint](https://www.biorxiv.org/content/10.1101/2025.11.18.689002v1) on bioRxiv. Please cite this manuscript as follows:

```{r, echo=T, eval=F, tidy=T}
citation("CroCoNet")
```