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multiomics-grn

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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

When to use

• Build enhancer-driven gene regulatory networks
• Integrate single-cell RNA-seq and ATAC-seq
• Identify eRegulons
• Analyze 10x multiome data
• Analyze paired scRNA+scATAC data
• Analyze unpaired scRNA+scATAC data
• Infer cis-regulatory GRNs
• Peak-to-gene linking

When not to use

• RNA-only regulons
• In silico TF perturbation

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