Index

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__call__() (evoaug.augment.AugmentBase method) (evoaug.augment.RandomDeletion method), [1] (evoaug.augment.RandomInsertion method), [1] (evoaug.augment.RandomInversion method) (evoaug.augment.RandomMutation method), [1] (evoaug.augment.RandomNoise method), [1] (evoaug.augment.RandomRC method), [1] (evoaug.augment.RandomTranslocation method), [1] __getitem__() (evoaug.evoaug.AugmentedGenomicDataset method) __init__() (evoaug.augment.RandomDeletion method), [1] (evoaug.augment.RandomInsertion method), [1] (evoaug.augment.RandomInversion method) (evoaug.augment.RandomMutation method), [1] (evoaug.augment.RandomNoise method), [1] (evoaug.augment.RandomRC method), [1] (evoaug.augment.RandomTranslocation method), [1] (evoaug.evoaug.AugmentedGenomicDataset method) (evoaug.evoaug.RobustLoader method), [1] (evoaug_utils.model_zoo.Basset method) (evoaug_utils.model_zoo.CNN method) (evoaug_utils.model_zoo.DeepSTARR method) (evoaug_utils.model_zoo.DeepSTARRModel method) (evoaug_utils.utils.H5DataModule method)

__len__() (evoaug.evoaug.AugmentedGenomicDataset method)

A

A (evoaug_utils.utils.H5DataModule attribute) allow_zero_length_dataloader_with_multiple_devices (evoaug_utils.utils.H5DataModule attribute)

AugmentBase (class in evoaug.augment) AugmentedGenomicDataset (class in evoaug.evoaug)

B

Basset (class in evoaug_utils.model_zoo)

batch_size (evoaug_utils.utils.H5DataModule attribute)

C

calculate_aupr() (in module evoaug_utils.utils) calculate_auroc() (in module evoaug_utils.utils) calculate_mse() (in module evoaug_utils.utils) calculate_pearsonr() (in module evoaug_utils.utils)

calculate_spearmanr() (in module evoaug_utils.utils) CNN (class in evoaug_utils.model_zoo) configure_optimizer() (in module evoaug_utils.utils) configure_optimizers() (evoaug_utils.model_zoo.DeepSTARRModel method)

D

data_path (evoaug_utils.utils.H5DataModule attribute) DeepSTARR (class in evoaug_utils.model_zoo) DeepSTARRModel (class in evoaug_utils.model_zoo)

disable_augmentations() (evoaug.evoaug.AugmentedGenomicDataset method) (evoaug.evoaug.RobustLoader method), [1] downsample (evoaug_utils.utils.H5DataModule attribute)

E

enable_augmentations() (evoaug.evoaug.AugmentedGenomicDataset method) (evoaug.evoaug.RobustLoader method), [1] evaluate_model() (in module evoaug_utils.utils)

evoaug.augment module evoaug.evoaug module

F

forward() (evoaug_utils.model_zoo.Basset method) (evoaug_utils.model_zoo.CNN method) (evoaug_utils.model_zoo.DeepSTARR method) (evoaug_utils.model_zoo.DeepSTARRModel method)

G

get_fmaps() (in module evoaug_utils.utils) get_predictions() (in module evoaug_utils.utils)

get_which_conv_layers_transferred() (evoaug_utils.model_zoo.Basset method) (evoaug_utils.model_zoo.DeepSTARR method)

H

H5DataModule (class in evoaug_utils.utils)

L

L (evoaug_utils.utils.H5DataModule attribute)

M

make_directory() (in module evoaug_utils.utils) module evoaug.augment evoaug.evoaug

N

num_classes (evoaug_utils.utils.H5DataModule attribute)

P

prepare_data_per_node (evoaug_utils.utils.H5DataModule attribute)

R

RandomDeletion (class in evoaug.augment), [1] RandomInsertion (class in evoaug.augment), [1] RandomInversion (class in evoaug.augment) RandomMutation (class in evoaug.augment), [1]

RandomNoise (class in evoaug.augment), [1] RandomRC (class in evoaug.augment), [1] RandomTranslocation (class in evoaug.augment), [1] RobustLoader (class in evoaug.evoaug), [1]

S

set_augmentations() (evoaug.evoaug.RobustLoader method), [1]

setup() (evoaug_utils.utils.H5DataModule method)

T

test_dataloader() (evoaug_utils.utils.H5DataModule method) test_step() (evoaug_utils.model_zoo.DeepSTARRModel method)

train_dataloader() (evoaug_utils.utils.H5DataModule method) training_step() (evoaug_utils.model_zoo.DeepSTARRModel method) transpose (evoaug_utils.utils.H5DataModule attribute)

V

val_dataloader() (evoaug_utils.utils.H5DataModule method)

validation_step() (evoaug_utils.model_zoo.DeepSTARRModel method)

X

x (evoaug_utils.utils.H5DataModule attribute) x_test (evoaug_utils.utils.H5DataModule attribute)

x_train (evoaug_utils.utils.H5DataModule attribute) x_valid (evoaug_utils.utils.H5DataModule attribute)

Y

y (evoaug_utils.utils.H5DataModule attribute) y_test (evoaug_utils.utils.H5DataModule attribute)

y_train (evoaug_utils.utils.H5DataModule attribute) y_valid (evoaug_utils.utils.H5DataModule attribute)