An interactive explorer for single-cell transcriptomics data

Quick start
Demo datasets
Preparing your data
Launching cellxgene
Hosting cellxgene
Annotating data
Contributing (ideas or code)
Contact & finding help

Troubleshooting tips & tricks

I tried to pip install cellxgene and got a weird error I don’t understand

This may happen, especially as we work out bugs in our installation process! Please create a new Github issue, explain what you did, and include all the error messages you saw. It’d also be super helpful if you call pip freeze and include the full output alongside your issue.

I have a BIG dataset, how can I make cellxgene run as fast as possible?

If your dataset requires gigabytes of disk space, you may need to select an appropriate storage format in order to effectively utilize cellxgene. Tips and tricks:

I’m following the developer instructions and get an error about “missing files and directories” when trying to build the client

This is likely because you do not have node and npm installed, we recommend using nvm if you’re new to using these tools.