scellop: Cell Type Composition Explorer

Scellop (previously CellPop) is an interactive visualization tool for cell type compositions. Easily compare your cell type compositions with different visual encodings, filter and sort on metadata, and export for communication.

Why scellop?

Cell type populations are commonly shown with stacked bar charts. However, scaling the number of samples and cell types in these visualizations create issues with analyzing these charts. Scellop alleviates this by presenting a flexible heatmap and side views with extending layered bar charts.

Installs

Scellop is available on NPM and PyPI.

npm i scellop

pip install scellop

Demo

A demo is available here. How to use the ScellopComponent is shown here.

The main view and interactions:

Set-up

This project uses pnpm.

Install dependencies with:

pnpm install

Run the demo with:

pnpm run dev

Instructions for Python package are it's own contributing guidelines.

Team

HIDIVE Lab

• Thomas C. Smits (tsmits@hms.harvard.edu)
• Nikolay Akhmetov (nikolay_akhmetov@hms.harvard.edu)
• Tiffany Liaw (tiffany_liaw@hms.harvard.edu)
• Nils Gehlenborg (nils@hms.harvard.edu)

Paper

Our preprint is available here.

Please cite this work as follows:

Thomas C Smits, Nikolay Akhmetov, Tiffany S. Liaw, Mark S. Keller, Eric Moerth, Nils Gehlenborg (2025). scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data. arXiv preprint. https://10.48550/arXiv.2510.09554