Pertpy is a Python-based software framework created to streamline the analysis of large-scale single-cell perturbation experiments, such as genetic modifications or drug treatments. By integrating with the scverse ecosystem, it offers a modular suite of tools for metadata annotation, quality control, and the calculation of specialized perturbation spaces. The platform enhances efficiency through GPU acceleration and provides a unified structure for identifying differential gene expression and shifts in cell type composition. Researchers can use Pertpy to deconvolve complex biological responses, such as distinguishing between viability-dependent and independent drug effects. Furthermore, it facilitates the discovery of multicellular programs and the characterization of previously unannotated gene pathways across diverse disease states. Ultimately, the framework fosters more robust biological insights by connecting experimental readouts with extensive public biological databases and ontologies.
References:
- Heumos L, Ji Y, May L, et al. Pertpy: an end-to-end framework for perturbation analysis[J]. Nature Methods, 2025: 1-10.
