1. In silico gene perturbation with GRNs

CellOracle leverages the constructed GRN models to simulate signal propagation inside a cell. Using these calculations with the GRN models, we estimate the effects of gene perturbations.

The jupyter notebook files and data used in this tutorial are available here .

Python notebook

• Overview
  • Notebook file
  • Data
  • What you can do
  • Custom data class / object
• 0. Import libraries
• 1. Load data
• 2. Make predictive models for simulation
• 3. In silico TF perturbation analysis
• 4. Visualization
  • Caution: It is very important to find the optimal scale parameter.
    • 4.2. Vector field graph
  • 4.2.1 Find parameters for n_grid and min_mass
  • 4.2.2 Plot vector fields
• 5. [This step is optional] Compare simulation vector with development vectors
• 6. Focus on a single development lineage to interpret the results in detail