bio-workflows-grn-pipeline

What problem does it solve?

End-to-end pipeline to infer gene regulatory networks from processed single-cell data and simulate downstream perturbations, enabling end-to-end SCENIC workflows across RNA-only and multiome data.

Core Features & Use Cases

• RNA-only GRN inference with pySCENIC (GRNBoost2, RcisTarget, AUCell) to identify regulons and activity per cell.
• Multiome SCENIC+ path for enhancer-driven GRNs using cisTopic, pycistarget, and eGRN construction, plus CellOracle perturbation simulations.
• Use case: Apply to a paired scRNA-seq + scATAC-seq dataset to map regulatory programs and predict perturbation effects.

Quick Start

Run the end-to-end GRN pipeline on processed single-cell data to infer regulons, score activity, and simulate perturbations using pySCENIC and SCENIC+.