Linear Conditional Variational Autoencoder for CyTOF data.
- Linear_cytovae.py: Core model implementation
- cytovae_train_utils.py: Training utilities including optimizer setup, device management, and training loop
- FCLayers.py: Fully connected neural network layer components (used by core model)
- cytof_ann_loader.py: Data loader for AnnData objects containing CyTOF data
- batch_correction/: Batch correction analysis (Figure 5)
- oncogene_screen_validation/: Signalling modules in oncogene screen (Figure 3)
- size_model/: Size factor modeling and analysis (Figure 4)
- test_hyperparameters/: Hyperparameter testing on oncogene screen data (Figure 2)