Acknowledgements
Funding
This work was supported by the German Cancer Research Center (DKFZ) through a doctoral fellowship and by the Deparatment of Neuropathology Heidelberg.
Institutional support
ProteoPy was developed at:
Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Germany
German Cancer Research Center (DKFZ), Heidelberg, Germany
German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
We thank the following research groups for providing the scientific environment in which ProteoPy was developed:
The Bludau Lab and the Bioinformatics group within the Department of Neuropathology, University Hospital Heidelberg
The Gerstung Lab at the German Cancer Research Center (DKFZ), Heidelberg
Inspiration
ProteoPy’s API design draws direct inspiration from the
scanpy and
muon ecosystems. By adopting their
modular syntax (pp, tl, pl) and AnnData-centric workflow,
ProteoPy aims to provide a familiar and accessible interface for
researchers already working within the single-cell and multi-omics
community. We are grateful to the original authors and contributors of
scanpy — in particular Fabian Theis and
the Theis Lab
— and of muon — notably
Danila Bredikhin and the
Stegle Lab at EMBL and DKFZ
— for creating open,
well-designed frameworks that have shaped how the community interacts
with high-dimensional biological data.
Software dependencies
ProteoPy builds upon the excellent work of many open-source projects:
pandas for data manipulation
AnnData for annotated data structures
scanpy for single-cell analysis integration
Matplotlib and Seaborn for visualization
scikit-learn for machine learning utilities
We are grateful to the developers and maintainers of these projects for their contributions to the scientific Python ecosystem.
Contact
For correspondence regarding ProteoPy, please contact:
Isabell Bludau