Portable-CELLxGENE

Portable-CELLxGENE is a standalone version of CELLxGENE and CELLxGENE-gateway to allow single-cell transcriptomic data to be annotated without needing the command line or extra software.

Click to install

Click to reveal video of MacOS installation process

Having problems? Visit the installation page.

Running Portable-CELLxGENE

Click to reveal video of basic Portable-CELLxGENE usage

Recorded in MacOS, but the process is similar in Windows.

A file browser will open. Navigate to the folder containing your .h5ad and click “Open”.
A page listing the datasets should open in your browser. If it does not open after a minute, then navigate to http://127.0.0.1:5005/portable_home.html yourself. If the page opened automatically but is not displaying anything, then you may need to refresh it.
Follow the instructions on the homepage.
Once you are finished, close the CELLxGENE browser tab(s) and quit the app.

Note: Each annotation session will continue running in the background until either the Portable-CELLxGENE app is terminated or the session is closed from the “View running sessions” page (see end of above video). For large datasets, this may slow down your computer so it is advisable to terminate them once you are finished.

How to use CELLxGENE

There are many guides on how to use CELLxGENE available online, for example a basic introduction can be found here. The official documentation of CELLxGENE is here, which gives in-depth information on its use.