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UCSC Cell Browser

The UCSC Cell Browser is a fast, lightweight viewer for single-cell data. Cells are presented along withmetadata 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.

There is a UCSC Cell Browser website available at http://cells.ucsc.edu, which includes a handful of datasets from repositories like HCA, CIRM, and GEO as well as user contributed ones. We are happy to add your favorite dataset to this, you will just need to send us the files or a link to where we can download them to cells@ucsc.edu.

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.

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.

This is early research software. You are likely to run into bugs. 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.

.. toctree::
   :maxdepth: 1

   installation
   basic_usage
   internet
   tabsep
   seurat
   scanpy
   cellranger
   advanced
   markers
   combine
   cellbrowser_conf.rst
   dataDesc.rst
   requirements
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