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 Python 3.10–3.12 installed on your system.

How to install Rectangle:

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

pip install rectanglepy

Rectangle is available under a dual licence:

• Open-source licence: GNU General Public License v3.0 (GPLv3) → Free to use, modify, and redistribute as long as modifications and redistributions are also under GPLv3.

• Commercial licence: For companies and individuals who wish to use Rectangle in proprietary or closed-source applications, a separate commercial licence is available. See LICENCE_COM for details.

For commercial licensing enquiries, please contact: innovation-psb@uibk.ac.at

See the changelog.

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

For commercial licensing: innovation-psb@uibk.ac.at

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