Getting Started
API Reference
AugmentBase
AugmentBase.__call__()
RandomDeletion
RandomDeletion.__init__()
RandomDeletion.__call__()
RandomInsertion
RandomInsertion.__init__()
RandomInsertion.__call__()
RandomTranslocation
RandomTranslocation.__init__()
RandomTranslocation.__call__()
RandomInversion
RandomInversion.__init__()
RandomInversion.__call__()
RandomMutation
RandomMutation.__init__()
RandomMutation.__call__()
RandomRC
RandomRC.__init__()
RandomRC.__call__()
RandomNoise
RandomNoise.__init__()
RandomNoise.__call__()
AugmentedGenomicDataset
AugmentedGenomicDataset.__init__()
AugmentedGenomicDataset.__len__()
AugmentedGenomicDataset.__getitem__()
AugmentedGenomicDataset.enable_augmentations()
AugmentedGenomicDataset.disable_augmentations()
RobustLoader
RobustLoader.__init__()
RobustLoader.enable_augmentations()
RobustLoader.disable_augmentations()
RobustLoader.set_augmentations()
DeepSTARR
DeepSTARR.__init__()
DeepSTARR.get_which_conv_layers_transferred()
DeepSTARR.forward()
DeepSTARRModel
DeepSTARRModel.__init__()
DeepSTARRModel.forward()
DeepSTARRModel.training_step()
DeepSTARRModel.validation_step()
DeepSTARRModel.test_step()
DeepSTARRModel.configure_optimizers()
Basset
Basset.__init__()
Basset.get_which_conv_layers_transferred()
Basset.forward()
CNN
CNN.__init__()
CNN.forward()
H5DataModule
H5DataModule.data_path
H5DataModule.batch_size
H5DataModule.x
H5DataModule.y
H5DataModule.transpose
H5DataModule.downsample
H5DataModule.x_train
H5DataModule.y_train
H5DataModule.x_valid
H5DataModule.y_valid
H5DataModule.x_test
H5DataModule.y_test
H5DataModule.A
H5DataModule.L
H5DataModule.num_classes
H5DataModule.__init__()
H5DataModule.setup()
H5DataModule.train_dataloader()
H5DataModule.val_dataloader()
H5DataModule.test_dataloader()
evaluate_model()
get_predictions()
calculate_auroc()
calculate_aupr()
calculate_mse()
calculate_pearsonr()
calculate_spearmanr()
configure_optimizer()
get_fmaps()
make_directory()
Examples
evoaug
evoaug.augment
evoaug.evoaug
