The UCSC Cell Browser is a viewer for single cell data. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster-specific marker genes.

To look at a list of selected single cell datasets, see http://cells.ucsc.edu

To setup your own cell browser, from Cellranger, Seurat, Scanpy or text files (tsv/csv), or just a single cell expression matrix, read the documentation at http://cellbrowser.rtfd.io

If you want us to add a single cell dataset to the website http://cells.ucsc.edu, please contact us at [email protected]. We are happy to add any dataset.

This is a viewer for a static, precomputed layout. If you're looking for an interative layout, where you can move the cells around and run algorithsm interactively, try Chan-Zuckerberg's own cellxgene or Spring.

Apart from labs at UCSC, UCSF and Gladstone who host their data at cells.ucsc.edu, other groups have setup their own cell browsers:

• Alexander Misharin Lab, Northwester University, https://www.nupulmonary.org/resources/
• Accelerating Medicine Partnership Consortium, https://immunogenomics.io/cellbrowser/, used in <a href="https://www.biorxiv.org/content/10.1101/351130v1">Zhang et al. 2018</a> and <a href="https://www.biorxiv.org/content/10.1101/382846v1">Der et al. 2018</a>
• The Seurat3Wizard, demo at http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard, builds a cell browser as its last step

Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/.

This is early research software. You are likely to find bugs. Please open a Github ticket or email us at [email protected], we can usually fix them quickly.