pertpy#
Pertpy is a scverse ecosystem framework for analyzing large-scale single-cell perturbation experiments. It provides tools for harmonizing perturbation datasets, automating metadata annotation, calculating perturbation distances, and efficiently analyzing how cells respond to various stimuli like genetic modifications, drug treatments, and environmental changes.
For more details, see Pertpy: an end-to-end framework for perturbation analysis .
New to pertpy? Check out the installation guide.
The API reference contains a detailed description of the pertpy API.
The tutorials walk you through real-world applications of pertpy.
Need help? Reach out on our forum to get your questions answered!
Found a bug? Interested in improving pertpy? Checkout our GitHub for the latest developments.
Citation#
@article{Heumos2025,
author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa D. and Peidli, Stefan and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Pinto, Gonçalo and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir Ali and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
title = {Pertpy: an end-to-end framework for perturbation analysis},
journal = {Nature Methods},
year = {2025},
publisher = {Springer Nature},
doi = {10.1038/s41592-025-02909-7},
url = {https://doi.org/10.1038/s41592-025-02909-7},
issn = {1548-7105}
}
NumFOCUS#
pertpy is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
