bio-gene-regulatory-networks-perturbation-simulation - Simulate transcription factor perturbation effects
Simulates transcription factor perturbation effects and predicts transcriptional responses with CellOracle, Dynamo, GEARS, scGen, and CPA.
Tags
Updated: 2026-09-28gene regulatory networksperturbation simulationtranscription factorssingle-cell RNA-seqcell state predictionRNA velocityin silico perturbation
Capabilities
Typical Inputs
What this skill does
- Build context-specific GRNs
- Simulate TF knockout effects
- Simulate TF overexpression effects
- Predict cell-state shift direction
- Compute perturbation scores
- Apply vector-field perturbations
- Compare perturbation baselines
- Assess validation gaps
Inputs
- scRNA-seq data
- Chromatin accessibility prior
- Base GRN
- Cell-type clusters
- Low-dimensional embedding
- Pseudotime values
- Perturbation specification
- RNA-velocity estimate
- Training perturbation responses
Outputs
- Predicted cell-state shift directions
- Perturbation scores
- Transition probabilities
- Perturbed embeddings
- Baseline comparisons
- Vector-field perturbation state
Requirements
- Python environment
- CellOracle 0.18 or later
- scanpy 1.10 or later
- anndata 0.10 or later
- Dynamo 1.4 or later
- GEARS or CPA support
- Installed package API compatibility