scientific-perturbation-analysis

What problem does it solve?

This skill provides an end-to-end pipeline for analyzing perturbation data in single-cell experiments, leveraging pertpy, Augur, and scIB to integrate CRISPR screens, drug perturbations, and knockdown data.

Core Features & Use Cases

• Integrates perturb-seq CRISPR perturbations with scRNA-seq data to quantify perturbation effects across cell types.
• Offers differential perturbation analysis, Augur-based cell-type prioritization, and scGen-based in silico perturbation predictions, with scIB benchmarking to assess integration quality.
• Use Case: Compare treated vs control cells across multiple perturbations to identify robust, cell-type-specific responses.

Quick Start

Run the perturbation analysis workflow on your single-cell dataset using perturbpy to identify perturbation effects across cell types.