UCSC Cell Browser

The UCSC Cell Browser is a fast, lightweight viewer for single-cell data. Cells are presented along with metadata and gene expression, with the ability to color cells by both of these attributes. Additional information, such as cluster marker genes and selected dataset-relevant genes, can also be displayed.

The main UCSC Cell Browser website runs at http://cells.ucsc.edu, showing more than 330 datasets, the majority submitted directly to us from labs for publications. We are happy to host your datasets; to do so upload your files via the website https://cells-submit.gi.ucsc.edu. To not show data publicly, check the box “private dataset” in the upload interface. Email us at cells@ucsc.edu if you have any questions. We can also add datasets that are not yours, just email us a link to the publication.

If you use the UCSC Cell Browser in your research, please cite our Bioinformatics paper. If you are also using data from a specific dataset we host, please also cite the original authors of that dataset (visible under ‘Info & Download’ while viewing that dataset).

The UCSC Cell Browser is funded by grants from the California Institute for Regenerative Medicine and the Chan-Zuckerberg Initiative.

To report issues or view the source code, see GitHub.

If you do run into any trouble, please open a Github issue or email us at cells@ucsc.edu, we can usually fix them quickly.

Exploring Data

Already have a dataset open at https://cells.ucsc.edu or your own Cell Browser instance? Start here to learn how to navigate, search genes, select cells, and use features like split-screen comparison and heatmaps.

Using the Cell Browser

Submitting Data to the Cell Browser

Building Your Own Cell Browser

Want to create a Cell Browser for your own single-cell dataset and host it on your own web server? Follow the guides below.

Building a Cell Browser