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)
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 https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad
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.
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.