Pertpy: an end-to-end framework for perturbation analysis
Advances in single-cell technology have enabled the measurement of cell-resolved molecular states across a variety of cell lines and tissues under a plethora of genetic, chemical, environmental or disease perturbations. Current methods focus on differential comparison or are specific to a particular task in a multi-condition setting with purely statistical perspectives. The quickly growing number, size and complexity of such studies require a scalable analysis framework that takes existing biological context into account. Here we present pertpy, a Python-based modular framework for the analysis of large-scale single-cell perturbation experiments. Pertpy provides access to harmonized perturbation datasets and metadata databases along with numerous fast and user-friendly implementations of both established and novel methods, such as automatic metadata annotation or perturbation distances, to efficiently analyze perturbation data. As part of the scverse ecosystem, pertpy interoperates with existing single-cell analysis libraries and is designed to be easily extended.
Authors
- Lukas Heumos (ORCID: https://orcid.org/0000-0002-8937-3457)
- Eljas Roellin (ORCID: https://orcid.org/0009-0002-4181-5516)
- Stefan Peidli (ORCID: https://orcid.org/0000-0002-4257-8690)
- Johannes Ostner (ORCID: https://orcid.org/0000-0002-6448-9437)
- Gregor Sturm (ORCID: https://orcid.org/0000-0001-9584-7842)
- Zihe Zheng (ORCID: https://orcid.org/0000-0003-3248-2174)
- Karin Hrovatin (ORCID: https://orcid.org/0000-0003-3319-9645)
- Faye Chong (ORCID: https://orcid.org/0000-0002-5414-9746)
- L T May (ORCID: https://orcid.org/0009-0004-4337-2338)
- Tessa Green
- Amir Ali Moinfar (ORCID: https://orcid.org/0009-0005-4680-2724)
- Mingze Dong (ORCID: https://orcid.org/0000-0001-7367-6819)
- Michaela Müller (ORCID: https://orcid.org/0000-0002-1401-1785)
- Emma Dann (ORCID: https://orcid.org/0000-0002-7400-7438)
- Mohammad Nader Lotfollahi (ORCID: https://orcid.org/0000-0003-1067-225X)
- Ilan Gold (ORCID: https://orcid.org/0000-0002-5823-1026)
- Sergei Rybakov (ORCID: https://orcid.org/0000-0002-4944-6586)
- Altana Namsaraeva (ORCID: https://orcid.org/0000-0001-6071-9410)
- Mojtaba Bahrami (ORCID: https://orcid.org/0009-0003-0151-5196)
- Yuge Ji (ORCID: https://orcid.org/0009-0005-8198-9205)
- Alejandro Tejada
- Antonia Schumacher
- Herbert B. Schiller
- Fabian J. Theis
- Gonçalo Pinto
- Isra Mekki
- Xinyue Zhang
- Chris Sander
- Xichen Wu
Institutions
- Broad Institute (US)
- Boehringer Ingelheim (Germany) (DE)
- Pioneer (United States) (US)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- University of Cambridge (GB)
- Wellcome Sanger Institute (GB)
- Helmholtz Zentrum München (DE)
- LMU Klinikum (DE)
- Yale University (US)
- Humboldt-Universität zu Berlin (DE)
- German Center for Lung Research (DE)
- Dana-Farber/Harvard Cancer Center (US)
- European Molecular Biology Laboratory (DE)
- Technical University of Munich (DE)
- Charité - Universitätsmedizin Berlin (DE)
- Ludwig-Maximilians-Universität München (DE)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-12-31
- DOI
- https://doi.org/10.1038/s41592-025-02909-7
- Citations
- 5
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 4.03