Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-20T06:22:58.940Z
Answers.LastActivityDate: 2020-05-20T06:22:58.940Z
Answers.UserDisplayName: milanmlft
Body: <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>
  
Tags: <r><scrnaseq><seurat>
Title: Receptor-Ligand R-package for visualization
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  