bio-gene-regulatory-networks-multiomics-grn
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill multiomics-grn --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Cell Ranger 8.0+, MACS3 3.0+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Multiomics GRN Inference **"Build an enhancer-driven gene regulatory network from my multiome data"** → Integrate scRNA-seq and scATAC-seq to identify eRegulons: transcription factor-enhancer-target gene triplets linking TF binding to chromatin accessibility and gene expression changes. - Python: SCENIC+ pipeline with `scenicplus` for eRegulon assembly - Python: `pycisTopic` for topic modeling of scATAC-seq regions Build enhancer-driven gene regulatory networks from paired single-cell RNA-seq and ATAC-seq data. SCENIC+ extends SCENIC by linking TFs to their enhancers and target genes through eRegulons. ## SCENIC+ Overview | Component | Tool | Purpose | |-----------|
- Version Compatibility
- SCENIC+ Overview
- Input Preparation
- From 10x Multiome (CellRanger ARC)
- Call Peaks with MACS3
- Create cisTopic Object
- SCENIC+ Workflow
- eRegulon Interpretation
- eRegulon Activity Scoring
- Visualization
- FigR Alternative
- Resource Requirements
- Related Skills
What does the bio-gene-regulatory-networks-multiomics-grn skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill multiomics-grn --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.