sc-grn

What problem does it solve?

This Skill automates the complex and multi-step process of inferring gene regulatory networks (GRNs) from single-cell RNA sequencing data, which traditionally requires stitching together multiple bioinformatics tools.

Core Features & Use Cases

• Unified GRN Inference: Integrates pySCENIC (GRNBoost2, cisTarget, AUCell) for comprehensive GRN construction.
• Fallback Correlation Method: Provides a simpler correlation-based GRN inference when pySCENIC is unavailable.
• CellOracle Integration: Supports GRN simulation and perturbation analysis using CellOracle.
• Use Case: Analyze single-cell RNA-seq data to identify key transcription factors and their target genes that drive cell identity or response to stimuli.

Quick Start

Run the sc-grn skill to infer gene regulatory networks from the provided processed single-cell data file.