bio-workflows-grn-pipeline
End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only (pySCENIC) and multiome (SCENIC+) paths. Use when building gene regulatory networks from single-cell transcriptomic or multiome data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill grn-pipeline --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: anndata 0.10+, pandas 2.2+, scanpy 1.10+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Gene Regulatory Network Pipeline **"Infer gene regulatory networks from my single-cell data"** → Orchestrate pySCENIC regulon inference (GRNBoost2, cisTarget, AUCell), CellOracle perturbation simulation, and regulon-based cell type characterization. Complete workflow from processed single-cell data to regulon discovery and perturbation simulation. ## Pipeline Overview ``` Processed AnnData (QC'd, normalized, clustered) | +----- RNA only? -------> Path A: pySCENIC (3-step) | | | v | [1. GRNBoost2] ----> TF-target adjacencies | | | v | [2. RcisTarget] ---> Regulon pruning (motif enrichment) | | | v | [3. AUCell] -------> Regulon activity scoring | +----- Multiome? -------> Path B: SCENIC+ | | | v | [1. cisTopic] -----> Topic modeling on ATAC | | | v | [2. pyc
- Version Compatibility
- Pipeline Overview
- Path A: pySCENIC (RNA-Only)
- Step 1: GRN Inference with GRNBoost2
- Step 2: Regulon Pruning with RcisTarget
- Step 3: AUCell Activity Scoring
- QC Checkpoint: GRN Inference
- Path B: SCENIC+ (Multiome)
- Step 1: ATAC Topic Modeling with cisTopic
- Step 2: Enhancer-TF Mapping
- Step 3: eGRN Construction
- CellOracle Perturbation Simulation
- QC Checkpoint: Perturbation
- Complete Pipeline Script
What does the bio-workflows-grn-pipeline skill do?
End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only (pySCENIC) and multiome (SCENIC+) paths. Use when building gene regulatory networks from single-cell transcriptomic or multiome data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill grn-pipeline --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.