<p>Two nice tools for receptor-ligand interaction analysis are:</p>

<ul>
<li><a href="https://www.cellphonedb.org" rel="nofollow noreferrer">CellPhoneDB</a> by the Teichmann lab, although this is not an R package...</li>
<li><a href="https://github.com/saeyslab/nichenetr" rel="nofollow noreferrer">NicheNet</a> by the Saeys group</li>
</ul>

<p>Note that these tools are mainly meant for analysis of receptor-ligand interactions, although I think NicheNet also has some visualization options. CellPhoneDB needs to be run from a shell, but the results can easily be imported into R for visualization. You might check the papers on these 2 methods for some ideas of visualization. Combining Seurat's visualization options and ggplot2 should get you already pretty far.</p>

CC BY-SA 4.0
2020-05-20T06:22:58.940Z
2020-05-20T06:22:58.940Z
milanmlft
<p>I was wondering if there was any R-package for receptor-ligand interaction similar to SingleCellSignal (<a href="https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/SingleCellSignalR/vignettes/UsersGuide.Rmd" rel="nofollow noreferrer">https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/SingleCellSignalR/vignettes/UsersGuide.Rmd</a>)</p>

<p>+++ if there are vignettes and/or the graphs can be customized.</p>

<p>+++ if it can be linked to Seurat</p>

<p>Note: I have tried iTALK, but I keep getting an error that seems to be a common problem and have left a query. </p>

<p>Thanks</p>

<r><scrnaseq><seurat>
Receptor-Ligand R-package for visualization
# Receptor-Ligand R-package for visualization

(Asked by: username_0 on 2020-05-19)

I was wondering if there was any R-package for receptor-ligand interaction similar to SingleCellSignal (<https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/SingleCellSignalR/vignettes/UsersGuide.Rmd>)

+++ if there are vignettes and/or the graphs can be customized.

+++ if it can be linked to Seurat

Note: I have tried iTALK, but I keep getting an error that seems to be a common problem and have left a query.

Thanks

**Tags:** r, scrnaseq, seurat

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## 1 answers

### Answer by username_1 on 2020-05-20. Score: 1

Two nice tools for receptor-ligand interaction analysis are:

* [CellPhoneDB](https://www.cellphonedb.org) by the Teichmann lab, although this is not an R package...
* [NicheNet](https://github.com/saeyslab/nichenetr) by the Saeys group

Note that these tools are mainly meant for analysis of receptor-ligand interactions, although I think NicheNet also has some visualization options. CellPhoneDB needs to be run from a shell, but the results can easily be imported into R for visualization. You might check the papers on these 2 methods for some ideas of visualization. Combining Seurat's visualization options and ggplot2 should get you already pretty far.


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