bio-gene-regulatory-networks-perturbation-simulation

What problem does it solve?

Simulate transcription factor perturbations on cell state by integrating a base GRN constructed from accessible chromatin with scRNA-seq expression, enabling predictions of how TF knockouts or overexpression shift cell identities and trajectories.

Core Features & Use Cases

• GRN-informed perturbation modeling: combine chromatin-based TF-target links with expression data to simulate perturbations.
• End-to-end workflow: build base GRN, fit regression-based links per cell type, run knockout/overexpression simulations, and visualize embedding shifts.
• Use case: prioritize TF perturbations for differentiation studies or perturb-seq planning by ranking TFs by predicted impact.

Quick Start

Provide your preprocessed AnnData and base GRN data to simulate a transcription factor perturbation and view predicted cell-state shifts.