pertpy 0.10.0

Perturbation Analysis in the scverse ecosystem.

pertpy

Documentation

Please read the documentation.

Installation

We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS). No particular hardware beyond a standard laptop is required.

You can install pertpy in less than a minute via pip from PyPI:

pip install pertpy

if you want to use scCODA or tascCODA, please install pertpy as follows:

pip install 'pertpy[coda]'

If you want to use the differential gene expression interface, please install pertpy by running:

pip install 'pertpy[de]'

Citation

Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516