Pertpy is a Python-based modular framework for the analysis of large-scale single-cell perturbation experiments.
Pertpy is a scverse core 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.
Please read our associated manuscript "Pertpy: an end-to-end framework for perturbation analysis".
ehrapy is a modular open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data.
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.