Rectangle is an open-source Python package for single-cell-informed cell-type deconvolution of bulk and spatial transcriptomic data, which is part of the scverse ecosystem.

Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical signature building for fine-grained cell-type deconvolution, estimation and correction of unknown cellular content, and efficient handling of large-scale single-cell data during signature matrix computation.

Rectangle was developed to overcome the current challenges in cell-type deconvolution, providing a robust and accurate methodology while ensuring a low computational profile.

Please refer to the documentation. In particular, the

• Tutorials for a step-by-step guide on how to use Rectangle, and the

• API documentation.

You need to have Python 3.10 or higher installed on your system.

How to install Rectangle:

Install the latest release of Rectangle from PyPI https://pypi.org/project/rectanglepy/:

pip install rectanglepy

See the changelog.

If you found a bug, please use the issue tracker.

If you use Rectangle in your project, please cite: (TBA)