Tutorials

This section contains several detailed tutorials showcasing different aspects of CAMPA. See the Workflow documentation for a short introduction to the CAMPA workflow of creating and analysing CSLs.

These tutorials will be using an example 4i dataset to generate and analyse CSLs for unperturbed and Meayamycin-perturbed cells.

Tutorials

• Setup and download data
  • Download parameter files
  • Set up CAMPA config
  • Download example dataset
• Data representation
  • The MPPData class
  • Export and saving
  • Visualisation
  • Filter and subset data
  • Normalisation
  • Prepare for VAE training
• Dataset for training models
  • Create NNDataset
  • Use NNDataset
• Train and evaluate models
  • Experiment class handles config files
  • Running experiments with the high-level api
  • Running experiments with Estimator and Predictor
  • Plot results using ModelComparator
• Cluster data into CSLs
  • Prepare a subset of the data
  • Prepare full dataset for projecting cluster to it
  • Interactive clustering and annotation
  • Predict model on full data
• Extract features from CSLs
  • Extract features
  • Explore and plot extracted features