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bio-gene-regulatory-networks-multiomics-grn

Infer enhancer-driven gene regulatory networks from paired scRNA-seq and scATAC-seq data using SCENIC+.

Updated Aug 23, 2026
Search Tags:#multimodal#scrna-seq#scatac-seq#cis-regulatory#scenic-plus#eregulons#gene-regulatory-networks
One-click install
npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-gene-regulatory-networks-multiomics-grn-stellaromics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-gene-regulatory-networks-multiomics-grn
Source: https://github.com/stellaromics/fast-bioinfo/tree/main/.claude/agents/spatial-analysis/skills/bio-gene-regulatory-networks-multiomics-grn
Command: npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-gene-regulatory-networks-multiomics-grn-stellaromics

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking transcription factors to enhancers and target genes. Use when analyzing 10x multiome or paired scRNA+scATAC data to infer cis-regulatory GRNs.

Core Features & Use Cases

  • SCENIC+ pipeline to assemble enhancer-driven regulatory networks from paired scRNA-seq and scATAC-seq data.
  • Integrates RNA expression with chromatin accessibility via motif enrichment, region-to-gene linking, and eRegulon assembly.
  • Score eRegulon activity per cell and visualize results to reveal cell-type-specific regulatory programs.

Quick Start

Infer enhancer-driven gene regulatory networks from my paired scrna-seq and scatac-seq data using SCENIC+.

Frequently Asked Questions about bio-gene-regulatory-networks-multiomics-grn

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

FAQPage Schema
How do I infer enhancer-driven gene regulatory networks from paired scRNA-seq and scATAC-seq data?▼

SCENIC+ infers enhancer-driven gene regulatory networks from paired scRNA-seq and scATAC-seq data by integrating RNA expression with chromatin accessibility. It links transcription factors to enhancers and target genes to identify eRegulons.

What are eRegulons and how do they reveal cell-type-specific regulatory programs?▼

eRegulons are enhancer-driven gene regulatory networks linking transcription factors to target genes via cis-regulatory regions. SCENIC+ scores eRegulon activity per cell to visualize and reveal cell-type-specific regulatory programs.

Can I use SCENIC+ to analyze 10x multiome datasets for cis-regulatory GRNs?▼

Yes, SCENIC+ analyzes 10x multiome or paired scRNA+scATAC datasets to infer cis-regulatory GRNs. It assembles enhancer-driven regulatory networks using motif enrichment and region-to-gene linking.

Do I need pycisTopic and macs3 to preprocess scATAC-seq data before running SCENIC+?▼

SCENIC+ requires pycisTopic and optional tools like macs3 or Signac/ArchR for preprocessing. These tools help prepare scATAC-seq chromatin accessibility data before assembling eRegulons.

What is the best way to integrate scRNA-seq expression with scATAC-seq chromatin accessibility?▼

The best way to integrate scRNA-seq and scATAC-seq is using SCENIC+ for multiomics GRN inference. It combines motif enrichment, region-to-gene linking, and eRegulon assembly to score regulatory activity across cells.

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