an interactive explorer for single-cell transcriptomics data

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


flexible selections, coloring, and differential expression of your selected sets of cells

single-gene analyses (e.g. expression analysis)

quick start

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 pbmc3k.h5ad

Launch cellxgene

cellxgene launch pbmc3k.h5ad --open

To explore more datasets already formatted for cellxgene, see Data or visit Getting Started 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.