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


This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project. All code is freely available for reuse under the MIT license.

Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an extension could be directly contributed, which would make it available for a wider audience, or that it’s on our roadmap and under active development.

Please note that cellxgene does not have public APIs. Our development may break extensions. We will document changes to the code base but it is advised that extensions pin the version of cellxgene they develop against.

Example Reuse & extensions

cellxgene Gateway

cellxgene Gateway allows you to use with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available proxies requests to that server.

cellxgene-VIP (Visualization in Plugin)

cellxgene-VIP enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.


Galaxy is an open source, web-based platform for data intensive biomedical research. cellxgene can be accessed within Galaxy to view analyzed datasets. See also the relevant publication

Single Cell Portal

The Single Cell Portal is a data hosting and visualization service. cellxgene can be embedded as an additional view to complement the visualizations provided by the. Example.


FASTGenomics is a collaborative research platform that offers easy-to-use data management and reproducible analytics to drive single-cell research forward. Many of the publicly available datasets in FASTGenomics - as well as your private datasets - can be interactively explored with cellxgene. See also this example for data from Schulte-Schrepping et al. (Cell, 2020). Note that it is not necessary to create an account, anonymous login is permitted.