Getting Started

The UCSC Cell Browser is available at https://cells.ucsc.edu. Open it in any modern web browser — no software installation is needed.

When you first visit, you will see the dataset selection screen. From here you can browse available datasets, filter by organ or organism, read dataset abstracts, and open any dataset into the interactive viewer.

This guide will walk you through the main features of the interface. If you’re looking to build a Cell Browser for your own data, see Installation instead.

What You Can Do

With the Cell Browser web interface you can:

• Browse and filter hundreds of curated single-cell datasets

• View cells on 2D scatter plots (tSNE, UMAP, or other layouts)

• Color cells by metadata annotations (cell type, age, condition, etc.)

• Search for any gene and color cells by expression level

• Select groups of cells and view violin plots of gene expression

• Compare annotations or genes side-by-side with split-screen mode

• View expression heatmaps across clusters

• Explore spatial transcriptomics data (Visium, MERFISH)

• Download expression matrices and metadata for further analysis

Try It Now

Open cortex-dev.cells.ucsc.edu to follow along with the examples in this guide. This dataset from Nowakowski et al. 2017 demonstrates most Cell Browser features.