Quick start

Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.

To install cellxgene you need Python 3.6+. We recommend installing cellxgene into a conda or virtual environment.

Install the package.

pip install cellxgene

Download an example anndata file

curl -o tabula-muris.h5ad https://cellxgene-example-data.czi.technology/tabula-muris.h5ad.zip
unzip tabula-muris.h5ad.zip

Launch cellxgene

cellxgene launch tabula-muris.h5ad --open

To explore more datasets already formatted for cellxgene, check out the Demo data or see Preparing your data to learn more about formatting your own data for cellxgene.

Getting help

We’d love to hear from you!

For questions, suggestions, or accolades, join the #cellxgene-users channel on the CZI Science Slack and say “hi!”.

For any errors, report bugs on Github.