An interactive explorer for single-cell transcriptomics data

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

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

Launch cellxgene with an example anndata file

cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad

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.