scenic-grn-inference

What problem does it solve?

Automates the inference of TF→region→gene regulatory relationships from paired scRNA-seq and scATAC-seq data, enabling mechanistic insights into gene regulation.

Core Features & Use Cases

• SCENIC+ based GRN inference from multiome data, producing eRegulons (TF→region→gene) with motif enrichment and GBM scoring.
• Supports both paired multiome data and unpaired RNA/ATAC data using metacell sampling to build pseudo-multiome representations.
• Flexible workflows via Snakemake and a Python API for interactive exploration, with options to customize cisTarget databases and metadata preparation.
• Use cases include decoding tissue-specific regulatory programs, comparing conditions, and prioritizing TF-region-gene triplets for experimental validation.

Quick Start

Prepare scRNA-seq and scATAC-seq data, configure SCENIC+ with cisTarget databases, and run the Snakemake pipeline or Python API to generate eRegulons.