Index

_

__init__() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) (Compocyte.core.models.dense_torch.DenseTorch method) (Compocyte.core.models.dummy_classifier.DummyClassifier method) (Compocyte.core.models.fit_methods.DaskBatchDataset method) (Compocyte.core.models.log_reg.LogisticRegression method) (Compocyte.core.models.trees.BoostedTrees method) (Compocyte.core.tools.Hierarchical_Metric method) (Compocyte.core.tuner.Tuner method)

A

add_variables() (Compocyte.core.base.data_base.DataBase method)

augmented_set_of_node_n() (Compocyte.core.tools.Hierarchical_Metric method)

B

BoostedTrees (class in Compocyte.core.models.trees)

C

calculate_intersects() (Compocyte.core.tools.Hierarchical_Metric method) check_for_counts() (Compocyte.core.base.data_base.DataBase method) Compocyte module Compocyte.core module Compocyte.core.base module Compocyte.core.base.data_base module Compocyte.core.base.export_import_base module Compocyte.core.base.hierarchy_base module Compocyte.core.hierarchical_classifier module Compocyte.core.models module

Compocyte.core.models.dense_torch module Compocyte.core.models.dummy_classifier module Compocyte.core.models.fit_methods module Compocyte.core.models.log_reg module Compocyte.core.models.trees module Compocyte.core.tools module Compocyte.core.tuner module Compocyte.data module Compocyte.pretrained module create_local_classifier() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

D

DaskBatchDataset (class in Compocyte.core.models.fit_methods) DataBase (class in Compocyte.core.base.data_base) dataloaders_from_dask() (in module Compocyte.core.models.fit_methods) dataloaders_from_dense() (in module Compocyte.core.models.fit_methods)

delete_dict_entries() (in module Compocyte.core.tools) DenseTorch (class in Compocyte.core.models.dense_torch) dict_depth() (in module Compocyte.core.tools) DummyClassifier (class in Compocyte.core.models.dummy_classifier)

E

ensure_depth_match() (Compocyte.core.base.hierarchy_base.HierarchyBase method) ensure_normlog() (Compocyte.core.base.data_base.DataBase method) ensure_not_view() (Compocyte.core.base.data_base.DataBase method)

ensure_unique_nodes() (Compocyte.core.base.hierarchy_base.HierarchyBase method) export_classifiers() (Compocyte.core.base.export_import_base.ExportImportBase method) ExportImportBase (class in Compocyte.core.base.export_import_base)

F

fit() (Compocyte.core.models.dummy_classifier.DummyClassifier method) (in module Compocyte.core.models.fit_methods) fit_logreg() (in module Compocyte.core.models.fit_methods) fit_torch() (in module Compocyte.core.models.fit_methods)

fit_trees() (in module Compocyte.core.models.fit_methods) flatten_dict() (in module Compocyte.core.tools) flatten_labels() (in module Compocyte.core.tools) forward() (Compocyte.core.models.dense_torch.DenseTorch method)

G

get_best_trial() (Compocyte.core.tuner.Tuner method) get_child_nodes() (Compocyte.core.base.hierarchy_base.HierarchyBase method) get_children_obs_key() (Compocyte.core.base.hierarchy_base.HierarchyBase method) get_last_annotation() (in module Compocyte.core.tools)

get_leaf_nodes() (Compocyte.core.base.hierarchy_base.HierarchyBase method) (in module Compocyte.core.tools) get_parent_node() (Compocyte.core.base.hierarchy_base.HierarchyBase method) get_parent_obs_key() (Compocyte.core.base.hierarchy_base.HierarchyBase method)

H

hF() (Compocyte.core.tools.Hierarchical_Metric method) Hierarchical_Metric (class in Compocyte.core.tools) HierarchicalClassifier (class in Compocyte.core.hierarchical_classifier)

hierarchy_names_unique() (in module Compocyte.core.tools) HierarchyBase (class in Compocyte.core.base.hierarchy_base) hP() (Compocyte.core.tools.Hierarchical_Metric method) hR() (Compocyte.core.tools.Hierarchical_Metric method)

I

import_classifier() (Compocyte.core.base.export_import_base.ExportImportBase method) import_classifiers() (Compocyte.core.base.export_import_base.ExportImportBase method) import_external() (Compocyte.core.models.dense_torch.DenseTorch class method)

infer_dict() (in module Compocyte.core.tools) infer_levels() (in module Compocyte.core.tools) introduce_limit() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) is_counts() (in module Compocyte.core.tools)

L

limit_cells() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) list_micro_metrics() (Compocyte.core.tools.Hierarchical_Metric method)

load() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) load_adata() (Compocyte.core.base.data_base.DataBase method) LogisticRegression (class in Compocyte.core.models.log_reg)

M

macro_hF() (Compocyte.core.tools.Hierarchical_Metric method) make_classifier_dict() (Compocyte.core.base.export_import_base.ExportImportBase method) make_classifier_graph() (Compocyte.core.base.hierarchy_base.HierarchyBase method) make_db() (Compocyte.core.tuner.Tuner method) make_entry() (Compocyte.core.tuner.Tuner method) make_graph_from_edges() (in module Compocyte.core.tools) module Compocyte Compocyte.core Compocyte.core.base Compocyte.core.base.data_base Compocyte.core.base.export_import_base Compocyte.core.base.hierarchy_base Compocyte.core.hierarchical_classifier Compocyte.core.models Compocyte.core.models.dense_torch Compocyte.core.models.dummy_classifier Compocyte.core.models.fit_methods Compocyte.core.models.log_reg Compocyte.core.models.trees Compocyte.core.tools Compocyte.core.tuner Compocyte.data Compocyte.pretrained

P

pbmc_pretrained() (in module Compocyte.pretrained) plot_hierarchy() (Compocyte.core.base.hierarchy_base.HierarchyBase method) predict() (Compocyte.core.models.dense_torch.DenseTorch method) (Compocyte.core.models.dummy_classifier.DummyClassifier method) (in module Compocyte.core.models.fit_methods) predict_all_child_nodes() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

predict_logits() (Compocyte.core.models.dense_torch.DenseTorch method) (Compocyte.core.models.dummy_classifier.DummyClassifier method) (Compocyte.core.models.log_reg.LogisticRegression method) (Compocyte.core.models.trees.BoostedTrees method) (in module Compocyte.core.models.fit_methods) predict_single_node() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

R

rename() (Compocyte.core.base.export_import_base.ExportImportBase method)

reset_output() (Compocyte.core.models.dense_torch.DenseTorch method) run_feature_selection() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

S

samples_per_class() (in module Compocyte.core.models.fit_methods) save() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) select_subset() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) select_subset_prediction() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

set_cell_relations() (Compocyte.core.base.hierarchy_base.HierarchyBase method) set_classifier_type() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) set_epoch() (Compocyte.core.models.fit_methods.DaskBatchDataset method) set_node_to_depth() (in module Compocyte.core.tools) set_threads() (in module Compocyte.core.models.fit_methods)

T

til_pretrained() (in module Compocyte.pretrained) to_categorical() (in module Compocyte.core.models.fit_methods) train_all_child_nodes() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method)

train_from_tuner() (Compocyte.core.tuner.Tuner method) train_single_node() (Compocyte.core.hierarchical_classifier.HierarchicalClassifier method) trial_run() (Compocyte.core.tuner.Tuner method) Tuner (class in Compocyte.core.tuner)

U

update_hierarchy() (Compocyte.core.base.hierarchy_base.HierarchyBase method)

V

variable_match_adata() (Compocyte.core.base.data_base.DataBase method)

Z

z_transform_properties() (in module Compocyte.core.tools)