Walkthroughs

• Seq Sim Workflow
  • 1. Imports
  • 2. Specify Number of Samples and Fold Change
  • 3. Specify Configuration File Parameters
  • 4. Generate and Save Sequencing Data
  • 5. Ensure files were saved properly
• SOM Example Iris
  • Basic Example of Using the Self-Organizing Map (SOM) Class
  • 1. Imports
  • 2. Load Data
  • 3. Train SOM
  • 4. Get Fit Metrics
  • 5. Plot SOM’s (see output directory for figures)
• SOM Example Seq
  • Application of Self-Organizing Maps (SOM) for Cell Type Identification
  • 1. Imports
  • 2. Load Data
  • 3. Train SOM
  • 4. Plot layout of SOM with neuron IDs
  • 5. Plot component planes and categorical data (see output directory for figures)
  • 6. Custom plotting for seq visualization for each neuron
• SOM Example Titanic
  • Hyperparameter Tuning Example for Self-Organizing Maps (SOM)
  • 1. Imports
  • 2. Load Data
  • 3. Define Hyperparameters
  • 4. Grid Search for Optimal Parameters
  • 5. Show the best parameters
  • 6. Train SOM
  • 7. Get the Fit Metrics
  • 8. Plot component planes and categorical data (see output directory for figures)