Pertpy: an end-to-end framework for perturbation analysis
Year: 2025
Type: article
Language: en
Topic: Single-cell and spatial transcriptomics
Authors and affiliations:
raw_author_name: Lukas Heumos
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
Research Unit Precision Regenerative Medicine (PRM), Comprehensive Pneumology Center (CPC); Member of the German Center for Lung Research (DZL), Munich, Germany
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
raw_author_name: Yuge Ji
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
raw_author_name: Lilly May
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
raw_author_name: Tessa D. Green
raw_affiliation_strings: Harvard Medical School, Ludwig Center at Harvard, DF/HCC Cancer Center, Broad Institute, Boston, MA, USA
raw_author_name: Stefan Peidli
raw_affiliation_strings: Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany
European Molecular Biology Laboratory, Heidelberg, Germany
Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
raw_author_name: Xinyue Zhang
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
raw_author_name: Xichen Wu
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
raw_author_name: Johannes Ostner
raw_affiliation_strings: Department of Statistics, LMU Munich, Munich, Germany
Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Antonia Schumacher
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Karin Hrovatin
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
raw_author_name: Michaela Müller
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Faye Chong
raw_affiliation_strings: Helmholtz Pioneer Campus, Munich, Germany
Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Gregor Sturm
raw_affiliation_strings: Boehringer Ingelheim International Pharma GmbH & Co. KG, Biberach, Germany
raw_author_name: Alejandro Tejada
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Emma Dann
raw_affiliation_strings: Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
raw_author_name: Mingze Dong
raw_affiliation_strings: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
raw_author_name: Gonçalo Pinto
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Mojtaba Bahrami
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
raw_author_name: Ilan Gold
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Sergei Rybakov
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
raw_author_name: Altana Namsaraeva
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
Konrad Zuse School of Excellence in Learning and Intelligent Systems (ELIZA), Darmstadt, Germany
raw_author_name: Amir Ali Moinfar
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
raw_author_name: Zihe Zheng
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Eljas Roellin
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
raw_author_name: Isra Mekki
raw_affiliation_strings: Helmholtz AI, Helmholtz Zentrum München, Munich, Germany
raw_author_name: Chris Sander
raw_affiliation_strings: Harvard Medical School, Ludwig Center at Harvard, DF/HCC Cancer Center, Broad Institute, Boston, MA, USA
raw_author_name: Mohammad Lotfollahi
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
raw_author_name: Herbert B. Schiller
raw_affiliation_strings: Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
Research Unit Precision Regenerative Medicine (PRM), Comprehensive Pneumology Center (CPC); Member of the German Center for Lung Research (DZL), Munich, Germany
raw_author_name: Fabian J. Theis
raw_affiliation_strings: Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany. fabian.theis@helmholtz-muenchen.de
School of Computation, Information and Technology, Technical University of Munich, Munich, Germany. fabian.theis@helmholtz-muenchen.de
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany. fabian.theis@helmholtz-muenchen.de