Index

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__abstractmethods__ (MyLogger attribute) __annotations__ (Individuality attribute) __dataclass_fields__ (Individuality attribute) __dataclass_params__ (Individuality attribute) __dict__ (Estimator attribute) (Individuality attribute) (TestIndividuality attribute) __doc__ (Abnormality attribute) (AbnormalityLitModule attribute) (AnnDataModule attribute) (AnnDatasetAE attribute) (AnnDatasetClf attribute) (Classifier attribute) (ClfLitModule attribute) (DefaultAE attribute) (DefaultCLF attribute) (DS attribute) (Estimator attribute) (Individuality attribute) (LitModule attribute) (MyLogger attribute) (TestIndividuality attribute) __eq__() (Individuality method) __getitem__() (AnnDataModule method) (AnnDatasetAE method) (AnnDatasetClf method) (DS method) __hash__ (Individuality attribute) __init__() (Abnormality method) (AbnormalityLitModule method) (AnnDataModule method) (AnnDatasetAE method) (AnnDatasetClf method) (Classifier method) (ClfLitModule method) (DefaultAE method) (DefaultCLF method) (DS method) (Estimator method) (Individuality method) (LitModule method) (MyLogger method) __len__() (AnnDataModule method) (AnnDatasetAE method) (AnnDatasetClf method) (DS method) __module__ (Abnormality attribute) (AbnormalityLitModule attribute) (AnnDataModule attribute) (AnnDatasetAE attribute) (AnnDatasetClf attribute) (Classifier attribute) (ClfLitModule attribute) (DefaultAE attribute) (DefaultCLF attribute) (DS attribute) (Estimator attribute) (Individuality attribute) (LitModule attribute) (MyLogger attribute) (TestIndividuality attribute)

__parameters__ (AnnDatasetAE attribute) (AnnDatasetClf attribute) (DS attribute) __post_init__() (Individuality method) __repr__() (Individuality method) __weakref__ (Estimator attribute) (Individuality attribute) (TestIndividuality attribute) _abc_impl (MyLogger attribute) _build_topology() (Individuality method) _check_args() (Individuality method) _configure_anndata_class() (Abnormality method) (Classifier method) (Estimator method) _default_litModule() (Abnormality method) (Classifier method) (Estimator method) _default_loss() (Abnormality method) (Classifier method) (Estimator method) _default_metric() (Abnormality method) (Classifier method) (Estimator method) _default_model() (Abnormality method) (Classifier method) (Estimator method) _fit() (Estimator method) _is_full_backward_hook (AbnormalityLitModule attribute) (ClfLitModule attribute) (DefaultAE attribute) (DefaultCLF attribute) (LitModule attribute) _predict() (Estimator method) _predict_step() (Abnormality method) (Classifier method) (Estimator method)

A

Abnormality (class in scQUEST.abnormality) AbnormalityLitModule (class in scQUEST.abnormality) aggregate() (Abnormality static method) aml_and_healthy() (in module scQUEST.dataset.datasets)

aml_annotated_celltypes() (in module scQUEST.dataset.datasets) AnnDataModule (class in scQUEST.data) AnnDatasetAE (class in scQUEST.data) AnnDatasetClf (class in scQUEST.data)

B

breastCancerAtlas() (in module scQUEST.dataset.datasets)

breastCancerAtlasRaw() (in module scQUEST.dataset.datasets)

C

Classifier (class in scQUEST.classifier) ClfLitModule (class in scQUEST.classifier)

compute_individuality() (Individuality static method) configure_optimizers() (LitModule method)

D

DefaultAE (class in scQUEST.abnormality) DefaultCLF (class in scQUEST.classifier) DS (class in scQUEST.data)

dummy_ad() (in module scQUEST.tests.test_abnormality) (in module scQUEST.tests.test_anndatasets) (in module scQUEST.tests.test_classifier) dummy_ad_ones() (in module scQUEST.tests.test_abnormality)

E

Estimator (class in scQUEST.utils)

estimator (Classifier attribute) experiment (MyLogger property)

F

finalize() (MyLogger method) fit() (Abnormality method) (Classifier method) (Estimator method) forward() (AbnormalityLitModule method) (ClfLitModule method) (DefaultAE method) (DefaultCLF method) (LitModule method)

fruit_bowl() (in module scQUEST.tests.test_anndatasets)

G

get_n_groups_data() (in module scQUEST.tests.test_individuality) get_n_groups_feat() (in module scQUEST.tests.test_individuality)

get_n_groups_label() (in module scQUEST.tests.test_individuality) graph (Individuality attribute), [1] graph_type (Individuality attribute), [1]

I

Individuality (class in scQUEST.individuality)

isCategorical() (in module scQUEST.utils)

L

LitModule (class in scQUEST.utils) log_hyperparams() (MyLogger method)

log_metrics() (LitModule method) (MyLogger method)

M

metric (Individuality attribute), [1] metric_params (Individuality attribute), [1] module scQUEST scQUEST.abnormality scQUEST.classifier scQUEST.data scQUEST.dataset scQUEST.dataset.datasets scQUEST.individuality scQUEST.tests scQUEST.tests.test_abnormality scQUEST.tests.test_anndatasets scQUEST.tests.test_classifier scQUEST.tests.test_dataset scQUEST.tests.test_individuality scQUEST.utils

MyLogger (class in scQUEST.utils)

N

n_neighbors (Individuality attribute), [1]

name (MyLogger property) nn_params (Individuality attribute), [1]

P

pairwise() (in module scQUEST.utils) predict() (Abnormality method) (Classifier method) (Estimator method) (Individuality method)

prior (Individuality attribute), [1]

R

radius (Individuality attribute), [1]

S

save() (MyLogger method) scQUEST module scQUEST.abnormality module scQUEST.classifier module scQUEST.data module scQUEST.dataset module scQUEST.dataset.datasets module scQUEST.individuality module

scQUEST.tests module scQUEST.tests.test_abnormality module scQUEST.tests.test_anndatasets module scQUEST.tests.test_classifier module scQUEST.tests.test_dataset module scQUEST.tests.test_individuality module scQUEST.utils module setup() (AnnDataModule method)

T

test_0_neighbors_exception() (TestIndividuality method) test_ae_dataloading() (in module scQUEST.tests.test_anndatasets) test_all_different_groups_probability() (TestIndividuality method) test_clf_dataloading() (in module scQUEST.tests.test_anndatasets) test_dataloader() (AnnDataModule method) test_default() (in module scQUEST.tests.test_abnormality) (in module scQUEST.tests.test_classifier) test_download() (in module scQUEST.tests.test_dataset) test_homogenous_groups() (TestIndividuality method) test_litModule_load() (in module scQUEST.tests.test_abnormality) (in module scQUEST.tests.test_classifier) test_load_from_disk() (in module scQUEST.tests.test_dataset) test_model_is_fitting() (in module scQUEST.tests.test_abnormality) test_model_load() (in module scQUEST.tests.test_abnormality) (in module scQUEST.tests.test_classifier)

test_non_numeric_labels() (TestIndividuality method) test_provide_graph() (TestIndividuality method) test_reproducible_model_init() (in module scQUEST.tests.test_abnormality) (in module scQUEST.tests.test_classifier) test_step() (LitModule method) test_two_groups_probability() (TestIndividuality method) TestIndividuality (class in scQUEST.tests.test_individuality) train_dataloader() (AnnDataModule method) training (AbnormalityLitModule attribute) (ClfLitModule attribute) (DefaultAE attribute) (DefaultCLF attribute) (LitModule attribute) training_step() (LitModule method)

V

val_dataloader() (AnnDataModule method)

validation_step() (LitModule method) version (MyLogger property)