Index

_

__call__() (phenonaut.integration.integrators.classic.Concatenate_ViewIntegrator method) (phenonaut.integration.integrators.classic.MVMDS_ViewIntegrator method) (phenonaut.integration.integrators.classic.SplitAutoencoder_ViewIntegrator method) (phenonaut.integration.integrators.Concatenate_ViewIntegrator method) (phenonaut.integration.integrators.MVMDS_ViewIntegrator method) (phenonaut.integration.integrators.SplitAutoencoder_ViewIntegrator method) (phenonaut.metrics.non_ds_phenotypic_metrics.PhenotypicMetric method) (phenonaut.packaged_datasets.metadata_moa.MetadataBROADLincsCellPaintingMOAs method) (phenonaut.packaged_datasets.metadata_moa.MetadataJUMPMOACompounds method) (phenonaut.predict.predictor_dataclasses.PhenonautPredictionMetric method) (phenonaut.transforms.dimensionality_reduction.LDA method) (phenonaut.transforms.dimensionality_reduction.PCA method) (phenonaut.transforms.dimensionality_reduction.TSNE method) (phenonaut.transforms.dimensionality_reduction.UMAP method) (phenonaut.transforms.preparative.RemoveHighestCorrelatedThenVIF method) (phenonaut.transforms.preparative.RemoveHighlyCorrelated method) (phenonaut.transforms.preparative.VIF method) (phenonaut.transforms.transformer.Transformer method)

A

add() (phenonaut.output.scatter.Scatter method) add_clinical_decision_data_to_df() (phenonaut.packaged_datasets.tcga.TCGA method) add_image_slide() (phenonaut.output.pptx.PhenonautPPTX method) add_well_id() (phenonaut.data.dataset.Dataset method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) (phenonaut.workflow.Workflow method)

aggregate_dataset() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) append() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) auroc() (in module phenonaut.metrics)

B

BreastCancer (class in phenonaut.packaged_datasets.breast_cancer)

C

calc_connectivity_scores() (in module phenonaut.metrics.non_ds_phenotypic_metrics) calc_spearmansrank_scores() (in module phenonaut.metrics.non_ds_phenotypic_metrics) calc_zhang_scores() (in module phenonaut.metrics.non_ds_phenotypic_metrics) calc_zhang_scores_all_v_all() (in module phenonaut.metrics.non_ds_phenotypic_metrics) callable_args (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) check_path() (in module phenonaut.utils) choices (phenonaut.predict.predictor_dataclasses.HyperparameterCategorical attribute) cityblock_distance() (phenonaut.workflow.Workflow method) classification (phenonaut.predict.predict_utils.PredictionType attribute) clone_dataset() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method)

CMAP (class in phenonaut.packaged_datasets.cmap) CMAP_Level4 (class in phenonaut.packaged_datasets.cmap) combine_datasets() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) concatenate_datasets_horizontally() (in module phenonaut.integration) Concatenate_ViewIntegrator (class in phenonaut.integration.integrators) (class in phenonaut.integration.integrators.classic) conditional_hyperparameter_generator (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) conditional_hyperparameter_generator_constructor_keyword (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) constructor_kwargs (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) copy() (phenonaut.data.dataset.Dataset method) copy_column() (phenonaut.workflow.Workflow method)

D

data (phenonaut.data.dataset.Dataset property) (phenonaut.Phenonaut property) (phenonaut.phenonaut.Phenonaut property) Dataset (class in phenonaut.data.dataset) dataset_intersection() (in module phenonaut) dataset_size_cutoff (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) DAVE (class in phenonaut.predict.default_predictors.pytorch_models.dave) describe() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) description (phenonaut.data.dataset.TransformationHistory attribute) df (phenonaut.Phenonaut property) (phenonaut.phenonaut.Phenonaut property) df_keys() (phenonaut.packaged_datasets.base.PackagedDataset method)

df_to_csv() (phenonaut.data.dataset.Dataset method) df_to_multiple_csvs() (phenonaut.data.dataset.Dataset method) distance() (phenonaut.metrics.non_ds_phenotypic_metrics.PhenotypicMetric method) distance_df() (phenonaut.data.dataset.Dataset method) divide_mean() (phenonaut.data.dataset.Dataset method) divide_median() (phenonaut.data.dataset.Dataset method) drop_absent_features() (phenonaut.data.dataset.Dataset method) drop_columns() (phenonaut.data.dataset.Dataset method) drop_nans_with_cutoff() (phenonaut.data.dataset.Dataset method) drop_rows() (phenonaut.data.dataset.Dataset method) ds (phenonaut.Phenonaut property) (phenonaut.phenonaut.Phenonaut property) ds_keys() (phenonaut.packaged_datasets.base.PackagedDataset method)

E

embed_in_results (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) euclidean() (in module phenonaut.metrics) (in module phenonaut.metrics.distances)

euclidean_distance() (phenonaut.workflow.Workflow method)

F

feature_correlation_to_target() (in module phenonaut.metrics) (in module phenonaut.metrics.measures) features (phenonaut.data.dataset.Dataset property) (phenonaut.data.dataset.TransformationHistory attribute) files (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute) filter() (phenonaut.transforms.preparative.RemoveHighestCorrelatedThenVIF method) (phenonaut.transforms.preparative.RemoveHighlyCorrelated method) (phenonaut.transforms.preparative.VIF method) filter_columns() (phenonaut.data.dataset.Dataset method) (phenonaut.workflow.Workflow method) filter_columns_with_prefix() (phenonaut.data.dataset.Dataset method) filter_correlated_and_VIF_features() (phenonaut.workflow.Workflow method) filter_correlated_features() (phenonaut.workflow.Workflow method) filter_datasets_on_identifiers() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method)

filter_inplace() (phenonaut.data.dataset.Dataset method) filter_on_identifiers() (phenonaut.data.dataset.Dataset method) filter_rows() (phenonaut.data.dataset.Dataset method) (phenonaut.workflow.Workflow method) fit() (phenonaut.integration.integrators.base.ViewIntegrator method) (phenonaut.predict.default_predictors.pytorch_models.dave.DAVE method) (phenonaut.predict.default_predictors.pytorch_models.multiregressor_nn.MultiRegressorNN method) (phenonaut.transforms.supervised_transformer.SupervisedTransformer method) (phenonaut.transforms.transformer.Transformer method) fit_train_test_transform_test() (phenonaut.integration.integrators.base.ViewIntegrator method) fit_transform() (phenonaut.integration.integrators.base.ViewIntegrator method) (phenonaut.transforms.supervised_transformer.SupervisedTransformer method) (phenonaut.transforms.transformer.Transformer method) func (phenonaut.predict.predictor_dataclasses.PhenonautPredictionMetric attribute)

G

get_best_predictor_dataset_df() (in module phenonaut.predict.predict_utils) get_cdu_performance_df() (in module phenonaut.metrics) get_common_indexes() (in module phenonaut.predict.predict_utils) get_compound_locations() (phenonaut.data.platemap_querier.PlatemapQuerier method) (phenonaut.PlatemapQuerier method) get_dataset_combinations() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) get_dataset_index_from_name() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) get_dataset_names() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) get_df() (phenonaut.packaged_datasets.base.PackagedDataset method) (phenonaut.packaged_datasets.breast_cancer.BreastCancer method) (phenonaut.packaged_datasets.cmap.CMAP method) (phenonaut.packaged_datasets.cmap.CMAP_Level4 method) (phenonaut.packaged_datasets.iris.Iris method) (phenonaut.packaged_datasets.iris.Iris_2_views method) (phenonaut.packaged_datasets.lincs.LINCS_Cell_Painting method) (phenonaut.packaged_datasets.metadata_moa.MetadataBROADLincsCellPaintingMOAs method) (phenonaut.packaged_datasets.metadata_moa.MetadataJUMPMOACompounds method) (phenonaut.packaged_datasets.tcga.TCGA method) get_df_features_perturbation_column() (phenonaut.data.dataset.Dataset method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) get_df_from_optuna_db() (in module phenonaut.predict.predict_utils)

get_ds() (phenonaut.packaged_datasets.base.PackagedDataset method) (phenonaut.packaged_datasets.breast_cancer.BreastCancer method) (phenonaut.packaged_datasets.cmap.CMAP method) (phenonaut.packaged_datasets.cmap.CMAP_Level4 method) (phenonaut.packaged_datasets.iris.Iris method) (phenonaut.packaged_datasets.iris.Iris_2_views method) (phenonaut.packaged_datasets.lincs.LINCS_Cell_Painting method) (phenonaut.packaged_datasets.metadata_moa.MetadataBROADLincsCellPaintingMOAs method) (phenonaut.packaged_datasets.metadata_moa.MetadataJUMPMOACompounds method) (phenonaut.packaged_datasets.tcga.TCGA method) get_ds_from_query() (phenonaut.data.dataset.Dataset method) get_feature_ranges() (phenonaut.data.dataset.Dataset method) get_hash_dictionary() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) get_history() (phenonaut.data.dataset.Dataset method) get_metric() (in module phenonaut.predict.predict_utils) get_non_feature_columns() (phenonaut.data.dataset.Dataset method) get_prediction_type_from_y() (in module phenonaut.predict.predict_utils) get_unique_perturbations() (phenonaut.data.dataset.Dataset method) get_unique_treatments() (phenonaut.data.dataset.Dataset method) get_vif_scores() (phenonaut.transforms.preparative.VIF method) get_X_y() (in module phenonaut.predict.predict_utils) get_y_from_target() (in module phenonaut.predict.predict_utils) groupby() (phenonaut.data.dataset.Dataset method) groupby_datasets() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method)

H

has_fit (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) has_fit_transform (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) has_transform (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) header_offset (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute)

history (phenonaut.data.dataset.Dataset property) HyperparameterCategorical (class in phenonaut.predict.predictor_dataclasses) HyperparameterFloat (class in phenonaut.predict.predictor_dataclasses) HyperparameterInt (class in phenonaut.predict.predictor_dataclasses) HyperparameterLog (class in phenonaut.predict.predictor_dataclasses)

I

if_blank_also_blank() (phenonaut.workflow.Workflow method) impute_nans() (phenonaut.data.dataset.Dataset method)

Iris (class in phenonaut.packaged_datasets.iris) Iris_2_views (class in phenonaut.packaged_datasets.iris) is_callable (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute)

K

keys() (phenonaut.packaged_datasets.base.PackagedDataset method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method)

KNNImputer (class in phenonaut.transforms.imputers)

L

LDA (class in phenonaut.transforms.dimensionality_reduction) LINCS_Cell_Painting (class in phenonaut.packaged_datasets.lincs) load() (in module phenonaut) (in module phenonaut.phenonaut) (phenonaut.Phenonaut class method) (phenonaut.phenonaut.Phenonaut class method) (phenonaut.workflow.Workflow method)

load_csv_kwargs (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute) load_dataset() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) load_dict() (in module phenonaut.utils) Log2 (class in phenonaut.transforms.generic_transformations) loss_function() (phenonaut.predict.default_predictors.pytorch_models.dave.DAVE method) lower_bound (phenonaut.predict.predictor_dataclasses.OptunaHyperparameterNumber attribute) lower_is_better (phenonaut.predict.predictor_dataclasses.PhenonautPredictionMetric attribute)

M

mahalanobis() (in module phenonaut.metrics) (in module phenonaut.metrics.distances) mahalanobis_distance() (phenonaut.workflow.Workflow method) make_scree_plot() (phenonaut.transforms.dimensionality_reduction.LDA method) manhattan() (in module phenonaut.metrics) (in module phenonaut.metrics.distances) manhattan_distance() (phenonaut.workflow.Workflow method) match_perturbation_columns() (in module phenonaut) (in module phenonaut.phenonaut) max_classes (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) max_optuna_trials (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) merge_datasets() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) merge_splits_to_single_views() (phenonaut.integration.integrators.base.ViewIntegrator static method) MetadataBROADLincsCellPaintingMOAs (class in phenonaut.packaged_datasets.metadata_moa) MetadataJUMPMOACompounds (class in phenonaut.packaged_datasets.metadata_moa) method (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) method_kwargs (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) module phenonaut phenonaut.data phenonaut.data.dataset phenonaut.data.platemap_querier phenonaut.data.recipes phenonaut.errors phenonaut.integration phenonaut.integration.integrators phenonaut.integration.integrators.base phenonaut.integration.integrators.classic phenonaut.metrics phenonaut.metrics.compactness phenonaut.metrics.compactness.pr phenonaut.metrics.distances phenonaut.metrics.distinctness phenonaut.metrics.distinctness.distinctness_measures phenonaut.metrics.measures phenonaut.metrics.non_ds_phenotypic_metrics phenonaut.metrics.utils phenonaut.output phenonaut.output.boxplot phenonaut.output.heatmap phenonaut.output.pair_plot phenonaut.output.pptx phenonaut.output.scatter phenonaut.output.spreadsheet phenonaut.output.visualisation_base phenonaut.packaged_datasets phenonaut.packaged_datasets.base phenonaut.packaged_datasets.breast_cancer phenonaut.packaged_datasets.cmap phenonaut.packaged_datasets.iris phenonaut.packaged_datasets.lincs phenonaut.packaged_datasets.metadata_moa phenonaut.packaged_datasets.tcga phenonaut.phenonaut phenonaut.predict phenonaut.predict.default_predictors phenonaut.predict.default_predictors.classifiers phenonaut.predict.default_predictors.multiregressors phenonaut.predict.default_predictors.pytorch_models phenonaut.predict.default_predictors.pytorch_models.dave phenonaut.predict.default_predictors.pytorch_models.multiregressor_nn phenonaut.predict.default_predictors.regressors phenonaut.predict.optuna_functions phenonaut.predict.predict_utils phenonaut.predict.predictor_dataclasses phenonaut.predict.profile phenonaut.transforms phenonaut.transforms.dimensionality_reduction phenonaut.transforms.generic_transformations phenonaut.transforms.imputers phenonaut.transforms.preparative phenonaut.transforms.supervised_transformer phenonaut.transforms.transformer phenonaut.utils phenonaut.workflow

mp_value_score() (in module phenonaut.metrics) (in module phenonaut.metrics.distinctness) (in module phenonaut.metrics.distinctness.distinctness_measures) multiplex_df() (phenonaut.integration.integrators.base.ViewIntegrator static method) multiplex_df_merge_single_samples() (phenonaut.integration.integrators.base.ViewIntegrator static method) MultiRegressorNN (class in phenonaut.predict.default_predictors.pytorch_models.multiregressor_nn) MVMDS_ViewIntegrator (class in phenonaut.integration.integrators) (class in phenonaut.integration.integrators.classic)

N

name (phenonaut.predict.predictor_dataclasses.OptunaHyperparameter attribute) (phenonaut.predict.predictor_dataclasses.PhenonautPredictionMetric attribute) (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) needed (phenonaut.predict.predictor_dataclasses.HyperparameterCategorical attribute) (phenonaut.predict.predictor_dataclasses.OptunaHyperparameterNumber attribute) new_aggregated_dataset() (phenonaut.data.dataset.Dataset method)

new_dataset_from_query() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) new_feature_names (phenonaut.transforms.supervised_transformer.SupervisedTransformer attribute) NotEnoughRowsError num_features (phenonaut.data.dataset.Dataset property) num_views (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute)

O

optuna (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) OptunaHyperparameter (class in phenonaut.predict.predictor_dataclasses)

OptunaHyperparameterNumber (class in phenonaut.predict.predictor_dataclasses) output_file_name (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute)

P

PackagedDataset (class in phenonaut.packaged_datasets.base) PCA (class in phenonaut.transforms.dimensionality_reduction) pca() (phenonaut.workflow.Workflow method) pcol (phenonaut.data.dataset.Dataset property) percent_compact() (in module phenonaut.metrics) (in module phenonaut.metrics.compactness) (in module phenonaut.metrics.compactness.pr) percent_compact_summarise_results() (in module phenonaut.metrics.utils) percent_replicating() (in module phenonaut.metrics) (in module phenonaut.metrics.compactness) (in module phenonaut.metrics.compactness.pr) percent_replicating_results_dataframe_to_95pct_confidence_interval() (in module phenonaut.metrics.utils) percent_replicating_results_dataframe_to_percentile_vs_percent_replicating() (in module phenonaut.metrics.utils) percent_replicating_summarise_results() (in module phenonaut.metrics.utils) pertmutation_test_distinct_from_query_group() (in module phenonaut.metrics) (in module phenonaut.metrics.distinctness) pertmutation_test_type2_distinct_from_query_group() (in module phenonaut.metrics) perturbation_column (phenonaut.data.dataset.Dataset property) phenonaut module Phenonaut (class in phenonaut) (class in phenonaut.phenonaut) phenonaut.data module phenonaut.data.dataset module phenonaut.data.platemap_querier module phenonaut.data.recipes module phenonaut.errors module phenonaut.integration module phenonaut.integration.integrators module phenonaut.integration.integrators.base module phenonaut.integration.integrators.classic module phenonaut.metrics module phenonaut.metrics.compactness module phenonaut.metrics.compactness.pr module phenonaut.metrics.distances module phenonaut.metrics.distinctness module phenonaut.metrics.distinctness.distinctness_measures module phenonaut.metrics.measures module phenonaut.metrics.non_ds_phenotypic_metrics module phenonaut.metrics.utils module phenonaut.output module phenonaut.output.boxplot module phenonaut.output.heatmap module phenonaut.output.pair_plot module phenonaut.output.pptx module phenonaut.output.scatter module phenonaut.output.spreadsheet module phenonaut.output.visualisation_base module phenonaut.packaged_datasets module phenonaut.packaged_datasets.base module

phenonaut.packaged_datasets.breast_cancer module phenonaut.packaged_datasets.cmap module phenonaut.packaged_datasets.iris module phenonaut.packaged_datasets.lincs module phenonaut.packaged_datasets.metadata_moa module phenonaut.packaged_datasets.tcga module phenonaut.phenonaut module phenonaut.predict module phenonaut.predict.default_predictors module phenonaut.predict.default_predictors.classifiers module phenonaut.predict.default_predictors.multiregressors module phenonaut.predict.default_predictors.pytorch_models module phenonaut.predict.default_predictors.pytorch_models.dave module phenonaut.predict.default_predictors.pytorch_models.multiregressor_nn module phenonaut.predict.default_predictors.regressors module phenonaut.predict.optuna_functions module phenonaut.predict.predict_utils module phenonaut.predict.predictor_dataclasses module phenonaut.predict.profile module phenonaut.transforms module phenonaut.transforms.dimensionality_reduction module phenonaut.transforms.generic_transformations module phenonaut.transforms.imputers module phenonaut.transforms.preparative module phenonaut.transforms.supervised_transformer module phenonaut.transforms.transformer module phenonaut.utils module phenonaut.workflow module PhenonautPPTX (class in phenonaut.output.pptx) PhenonautPredictionMetric (class in phenonaut.predict.predictor_dataclasses) PhenonautPredictor (class in phenonaut.predict.predictor_dataclasses) PhenonautVisualisation (class in phenonaut.output.visualisation_base) PhenotypicMetric (class in phenonaut.metrics.non_ds_phenotypic_metrics) PheTransformerFitQueryMatchedNoRows pivot() (phenonaut.data.dataset.Dataset method) plate_to_cpd_to_well_dict (phenonaut.data.platemap_querier.PlatemapQuerier attribute) (phenonaut.PlatemapQuerier attribute) platemap_files (phenonaut.data.platemap_querier.PlatemapQuerier attribute) (phenonaut.PlatemapQuerier attribute) PlatemapQuerier (class in phenonaut) (class in phenonaut.data.platemap_querier) predict() (in module phenonaut.workflow) (phenonaut.predict.default_predictors.pytorch_models.dave.DAVE method) (phenonaut.predict.default_predictors.pytorch_models.multiregressor_nn.MultiRegressorNN method) PredictionType (class in phenonaut.predict.predict_utils) predictor (phenonaut.predict.predictor_dataclasses.PhenonautPredictor attribute) predictor_from_str() (in module phenonaut.predict.optuna_functions) predictor_to_str() (in module phenonaut.predict.optuna_functions) profile() (in module phenonaut.predict.profile)

R

raw_data_dir (phenonaut.packaged_datasets.base.PackagedDataset property) register_df_key() (phenonaut.packaged_datasets.base.PackagedDataset method) register_ds_key() (phenonaut.packaged_datasets.base.PackagedDataset method) regression (phenonaut.predict.predict_utils.PredictionType attribute) remove_blocklist_features() (phenonaut.data.dataset.Dataset method) remove_features_with_outliers() (phenonaut.data.dataset.Dataset method) remove_low_variance_features() (phenonaut.data.dataset.Dataset method) RemoveHighestCorrelatedThenVIF (class in phenonaut.transforms.preparative) RemoveHighlyCorrelated (class in phenonaut.transforms.preparative) rename_column() (phenonaut.data.dataset.Dataset method) (phenonaut.workflow.Workflow method)

rename_columns() (phenonaut.data.dataset.Dataset method) (phenonaut.workflow.Workflow method) replace_str() (phenonaut.data.dataset.Dataset method) revert() (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) RFImputer (class in phenonaut.transforms.imputers) RobustMAD (class in phenonaut.transforms.preparative) root (phenonaut.packaged_datasets.base.PackagedDataset property) run_cdu_benchmarks() (in module phenonaut.metrics) run_optuna_opt() (in module phenonaut.predict.optuna_functions) run_optuna_opt_merge_folds() (in module phenonaut.predict.optuna_functions) run_workflow() (phenonaut.workflow.Workflow method)

S

save() (phenonaut.output.pptx.PhenonautPPTX method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) save_figure() (phenonaut.output.scatter.Scatter method) save_scree_plot() (phenonaut.transforms.dimensionality_reduction.PCA method) scalar_projection() (in module phenonaut.metrics) (in module phenonaut.metrics.measures) (phenonaut.workflow.Workflow method) scale() (phenonaut.metrics.non_ds_phenotypic_metrics.PhenotypicMetric method) Scatter (class in phenonaut.output.scatter) scatter() (phenonaut.workflow.Workflow method) set_perturbation_column() (phenonaut.workflow.Workflow method) show() (phenonaut.output.scatter.Scatter method) show_pair_plot() (in module phenonaut.output.pair_plot) shrink() (phenonaut.data.dataset.Dataset method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method)

silhouette_score() (in module phenonaut.metrics) (in module phenonaut.metrics.distinctness) (in module phenonaut.metrics.distinctness.distinctness_measures) similarity() (phenonaut.metrics.non_ds_phenotypic_metrics.PhenotypicMetric method) SimpleImputer (class in phenonaut.transforms.imputers) split_column() (phenonaut.data.dataset.Dataset method) SplitAutoencoder_ViewIntegrator (class in phenonaut.integration.integrators) (class in phenonaut.integration.integrators.classic) StandardScaler (class in phenonaut.transforms.preparative) subtract_func_results_on_features() (phenonaut.data.dataset.Dataset method) subtract_mean() (phenonaut.data.dataset.Dataset method) subtract_median() (phenonaut.data.dataset.Dataset method) subtract_median_perturbation() (phenonaut.data.dataset.Dataset method) (phenonaut.Phenonaut method) (phenonaut.phenonaut.Phenonaut method) SupervisedTransformer (class in phenonaut.transforms.supervised_transformer)

T

TCGA (class in phenonaut.packaged_datasets.tcga) TCGA.TCGA_MetadataTuple (class in phenonaut.packaged_datasets.tcga) transform() (phenonaut.integration.integrators.base.ViewIntegrator method) (phenonaut.transforms.supervised_transformer.SupervisedTransformer method) (phenonaut.transforms.transformer.Transformer method) TransformationHistory (class in phenonaut.data.dataset) Transformer (class in phenonaut.transforms.transformer)

transpose() (phenonaut.data.dataset.Dataset method) treatment_id (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute) treatment_lambda (phenonaut.packaged_datasets.tcga.TCGA.TCGA_MetadataTuple attribute) treatment_spread_euclidean() (in module phenonaut.metrics) (in module phenonaut.metrics.distances) TSNE (class in phenonaut.transforms.dimensionality_reduction) tsne() (phenonaut.workflow.Workflow method)

U

UMAP (class in phenonaut.transforms.dimensionality_reduction)

umap() (phenonaut.workflow.Workflow method) upper_bound (phenonaut.predict.predictor_dataclasses.OptunaHyperparameterNumber attribute)

V

view (phenonaut.predict.predict_utils.PredictionType attribute) ViewIntegrator (class in phenonaut.integration.integrators.base)

VIF (class in phenonaut.transforms.preparative) VIF_filter_features() (phenonaut.workflow.Workflow method)

W

Workflow (class in phenonaut.workflow) write_boxplot_to_file() (in module phenonaut.output.boxplot) write_cdu_json() (in module phenonaut.metrics)

write_csv() (phenonaut.workflow.Workflow method) write_heatmap_from_df() (in module phenonaut.output.heatmap) write_multiple_csvs() (phenonaut.workflow.Workflow method) write_xlsx() (in module phenonaut.output.spreadsheet)

Z

ZCA (class in phenonaut.transforms.preparative)