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

# scDiffCom

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scDiffCom stands for “single-cell Differential Communication” and infers
changes in intercellular communication between two biological conditions
from scRNA-seq data (as [Seurat](https://satijalab.org/seurat/)
objects). The package relies on an internal collection of
ligand-receptor interactions (available for human, mouse and rat)
retrieved from seven curated databases.

<details>

<summary>

Display LRI databases
</summary>

- [CellChat](https://github.com/jinworks/CellChat)
- [CellPhoneDB](https://www.cellphonedb.org/)
- [CellTalkDB](https://github.com/ZJUFanLab/CellTalkDB)
- [connectomeDB2020](https://github.com/forrest-lab/NATMI)
- [ICELLNET](https://github.com/soumelis-lab/ICELLNET)
- [NicheNet](https://github.com/saeyslab/nichenetr)
- [SingleCellSignalR](https://www.bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html)

</details>

 

## Installation

``` r
# Install the development version from GitHub
devtools::install_github("CyrilLagger/scDiffCom")

# Install release version from CRAN
install.packages("scDiffCom")
```

## Usage

As an introduction, please look at the
[documentation](https://cyrillagger.github.io/scDiffCom/) and this
[vignette](https://cyrillagger.github.io/scDiffCom/articles/scDiffCom-vignette.html).

For a concrete and large-scale project that used scDiffCom, please look
at [scagecom.org](https://scagecom.org/), our murine atlas of
age-related changes in intercellular communication.

## Citation

Please consider reading and citing our Nature Aging paper:
[here](https://www.nature.com/articles/s43587-023-00514-x).
