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CellChat Shiny App

This is CellChat's Shiny app docker container or standalone shiny app for our Cell-Cell Communication Atlas Explorer, which allows interactive exploration of the cell-cell communication that are analyzed by our CellChat R-package.

Running CellChat Shiny docker container:

docker pull ucigenomics/cellchatshiny:beta
docker run --name cellchatshiny -p 2020:3838 -d --restart unless-stopped -v /PATH_to_File/cellchat.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

NB: In Step III, you MUST specify the absolute path to the cellchat.rds file you saved by modifying the part /PATH_to_File/cellchat.rds in the above command.

Running multiple CellChat Shiny apps

To open two apps for simultaneously exploring cell-cell communication from two datasets, you would need to open a new instance of docker run, and assign a different container name (--name) and also host port (-p XXXX:3838). For example, here we create two apps for two CellChat objects cellchat_humanSkin_NL.rds and cellchat_humanSkin_LS.rds by running the command below in the terminal

docker pull ucigenomics/cellchatshiny:beta

docker run --name cellchatshiny_NL -p 2020:3838 -d --restart unless-stopped -v /Users/suoqinjin/Documents/CellChat/tutorial/cellchat_humanSkin_NL.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

docker run --name cellchatshiny_LS -p 2021:3838 -d --restart unless-stopped -v /Users/suoqinjin/Documents/CellChat/tutorial/cellchat_humanSkin_LS.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

We then can access the two CellChat apps using the two urls: http://localhost:2020/Cellchat and http://localhost:2021/Cellchat

Running CellChat standalone shiny app:

Currently this standalone shiny app can be only used in Linux system.

Help or Suggestion

If you have any question, comment or suggestion, please post it in the 'Issues' section or contact cellchat.package@gmail.com.

Docker command

The full docker commands are list here. Below are several common used.