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 1,600 datasets covering over 160 million cells, organized into 180 collections alongside 132 standalone datasets. The majority are 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

• Getting Started
  • What You Can Do
  • Try It Now
• Featured Datasets
• Browsing and Selecting Datasets
  • Dataset List
  • Dataset Information
  • Opening a Dataset
  • Dataset Collections
• The Visualization
  • Navigating the Scatter Plot
  • Cluster Labels
  • Switching Layouts
  • Coloring by Metadata
  • Coloring by Gene Expression
  • Gene Expression Plots (Dot Plots)
  • Spatial Transcriptomics Data
  • Keyboard Shortcuts
  • Menu Reference
• Cell Selection, Comparison, and Heatmaps
  • Selecting Cells
  • Exporting Selected Cells
  • Setting Background Cells
  • Split-Screen Comparison
  • Expression Heatmap
• Custom Annotations and Accounts
  • Creating a Custom Annotation
  • Managing Custom Annotations
  • Signing In
  • Syncing Annotations
  • Sharing Annotations
• Frequently Asked Questions

Downloading and Loading Data

• Downloading Data
• Loading a dataset
• Bulk downloads

Submitting Data to the Cell Browser

• Submitting data to the UCSC Cell Browser

Building a Cell Browser

• Building Your Own Cell Browser