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scientific-perturbation-analysis

Identify perturbation-driven changes in single-cell gene expression across treatments.

3|1|Updated Feb 11, 2026
Search Tags:#analysis#single-cell#scrna-seq#perturbation#pertpy#augur
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-perturbation-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-perturbation-analysis
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-perturbation-analysis
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-perturbation-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about scientific-perturbation-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze single-cell perturbation data from CRISPR screens?▼

To analyze single-cell perturbation data from CRISPR screens, this skill provides an end-to-end pipeline using pertpy and scanpy to identify perturbation-driven gene expression changes across cell types.

What is Augur cell-type prioritization in perturbation analysis?▼

Augur cell-type prioritization in single-cell perturbation analysis ranks cell types by their perturbation response magnitude. This skill applies Augur to identify robust, cell-type-specific responses across treatments.

Can I use this skill for drug perturbation and knockdown experiments?▼

Yes, this skill applies to drug perturbation and knockdown experiments. It quantifies cell-type specific responses and assesses reproducibility across batches using scIB benchmarking.

Do I need pertpy and anndata installed to run scRNA-seq perturbation analysis?▼

Yes, scRNA-seq perturbation analysis requires the pertpy, scanpy, anndata, and pandas Python libraries. These dependencies are necessary to read, preprocess, analyze, and summarize differential perturbation effects.

What is the best way to benchmark integration quality in single-cell perturbation data?▼

To benchmark integration quality in single-cell perturbation data, this skill uses scIB. It applies scIB benchmarking to assess integration quality when combining CRISPR screens, drug perturbations, and knockdown data.

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