Index

_

__call__() (Composition method) (SpatialAutocorrelation method) __init__() (SmartLeiden method) (SmartPca method) (SmartScaler method) (SmartUmap method)

A

anndata_from_expression_csv() (in module tissuemosaic.io.read_anndata_from_csv)

are_dicts_equal() (in module tissuemosaic.utils.dict_util)

B

BaseEstimator (class in tissuemosaic.models.classifier_regressor.scikit_learn_interface)

C

cell_type_ids (GeneDataset attribute) cell_type_mapping (GeneDataset attribute) cell_type_props (GeneDataset attribute) cluster() (SmartLeiden method)

Composition (class in tissuemosaic.models.patch_analyzer.patch_analyzer) compute_distance_embedding() (in module tissuemosaic.utils.validation_util) concatenate_list_of_dict() (in module tissuemosaic.utils.dict_util) counts (GeneDataset attribute) covariates (GeneDataset attribute)

D

describe() (GeneDataset method)

download_from_bucket() (in module tissuemosaic.io.download)

E

explained_variance_ (SmartPca property)

explained_variance_ratio_ (SmartPca property)

F

fit() (MlpClassifier method) (MlpRegressor method) (SmartPca method) (SmartScaler method) (SmartUmap method)

fit_transform() (SmartPca method) (SmartScaler method) (SmartUmap method) flatten_dict() (in module tissuemosaic.utils.dict_util)

G

gene_names (GeneDataset attribute) GeneDataset (class in tissuemosaic.genex.gene_utils) get_distances() (SmartUmap method)

get_graph() (SmartUmap method) get_percentile() (in module tissuemosaic.utils.validation_util) get_z_score() (in module tissuemosaic.utils.validation_util)

I

inspect_dict() (in module tissuemosaic.utils.dict_util) inverse_one_hot() (in module tissuemosaic.utils.validation_util) is_classifier (MlpClassifier property) (MlpRegressor property)

is_regressor (MlpClassifier property) (MlpRegressor property)

K

k_cell_types (GeneDataset attribute)

M

make_gene_dataset_from_anndata() (in module tissuemosaic.genex.gene_utils) MlpClassifier (class in tissuemosaic.models.classifier_regressor.scikit_learn_interface) MlpRegressor (class in tissuemosaic.models.classifier_regressor.scikit_learn_interface) module tissuemosaic.genex.gene_utils tissuemosaic.genex.gene_visualization tissuemosaic.io.download tissuemosaic.io.read_anndata_from_csv tissuemosaic.utils.dict_util tissuemosaic.utils.validation_util

P

plot_gene_hist() (in module tissuemosaic.genex.gene_visualization) predict() (MlpClassifier method) (MlpRegressor method)

predict_log_proba() (MlpClassifier method) predict_proba() (MlpClassifier method)

S

score() (MlpClassifier method) (MlpRegressor method) SmartLeiden (class in tissuemosaic.utils.validation_util) SmartPca (class in tissuemosaic.utils.validation_util) SmartScaler (class in tissuemosaic.utils.validation_util)

SmartUmap (class in tissuemosaic.utils.validation_util) sort_dict_according_to_indices() (in module tissuemosaic.utils.dict_util) SpatialAutocorrelation (class in tissuemosaic.models.patch_analyzer.patch_analyzer) subset_dict() (in module tissuemosaic.utils.dict_util) subset_dict_non_overlapping_patches() (in module tissuemosaic.utils.dict_util)

T

tissuemosaic.genex.gene_utils module tissuemosaic.genex.gene_visualization module tissuemosaic.io.download module tissuemosaic.io.read_anndata_from_csv module

tissuemosaic.utils.dict_util module tissuemosaic.utils.validation_util module train_test_val_split() (in module tissuemosaic.genex.gene_utils) transfer_annotations_between_dict() (in module tissuemosaic.utils.dict_util) transform() (SmartPca method) (SmartScaler method) (SmartUmap method)