Installation

Python

Celldega supports Python 3.11 and 3.12. Install it into the environment used by your Jupyter notebook:

pip install celldega

For Scanpy-backed marker dot plots and marker ranking:

pip install "celldega[scanpy]"

For image preprocessing, including adding an aligned H&E background:

pip install "celldega[pre]"

Image operations also require a working native libvips installation. See preprocessing and aligned H&E for the relevant workflows.

See Usage for notebook, web, and desktop options, then follow Getting Started or open an example notebook.

JavaScript

For an application managed with npm:

npm install celldega

import celldega from "celldega";

A standalone web page can import the built module or load it from a CDN such as esm.sh. See the JavaScript quick start for landscape, clustergram, and linked views.