Cell Guide 🧭

Navigate single-cell RNA-seq datasets in your web browser.

Try it at https://cell.guide

Features

• Display metadata on the UMAP figure
• Display gene expression on the UMAP figure
• Aggregate statistics for cell clusters and metadata categories
• Find any gene, instantly
• Browse statistics for every gene

Flip through metadata variables and see them in low-dimensional space.

See which donors have similar proportions of different cell clusters.

Find any gene and see expression across clusters, faceted by metadata variables.

Demo scRNA-seq data from the research article by Smillie et al. 2019.

Quick Start

Step 1. Install Cell Browser

We can install the Cell Browser Python package with pip (we need a specific version):

pip install cellbrowser==0.7.15

Or see the Cell Browser installation instructions.

Step 2. Create a browser for your data

See the documentation for how to create a Cell Browser for your data.

When your browser is working, it should look something like this:

Step 3. Copy Cell Guide files

# Get the Cell Guide code
curl -s https://codeload.github.com/slowkow/cellguide/tar.gz/master | tar xvz
 
# Overwrite the Cell Browser files: index.html js/ css/ ext/ img/
command cp -rf cellguide-master/www/* public_html/

For a complete example, see the demo.sh script.

Make sure to refresh your web browser with ⌘+Shift+R (or Ctrl+Shift+R on Windows).

Dependencies

The current version of Cell Guide depends on Cell Browser by Maximilian Haeussler.

Built with:

• Bootstrap
• CSS loaders
• d3-legend
• D3.js
• FastBitSet
• hcluster.js
• jQuery
• JSURL2
• pako
• palette.js
• papaparse
• tablesort

Let me know what you think! @slowkow