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 using the Cell Browser.

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 your dataset, you will just need to upload your files via the website https://cells-submit.gi.ucsc.edu. To not show data publicly, check the checkbox “private dataset” there. 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 then.

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 documentation on this website describes how you can create a Cell Browser for your own data and make it available through your own web server. This is rather rare, most users prefer to upload their data via https://cells-submit.gi.ucsc.edu as their dataset then automatically gets new features and the hosting is fast and stable.

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.