Index

_

__init__() (netmap.model.nbautoencoder.NegativeBinomialAutoencoder method) (netmap.model.nbautoencoder.NegativeBinomialLoss method) (netmap.model.standardautoencoder.Autoencoder method) (netmap.model.standardautoencoder.LogCoshLoss method) (netmap.model.standardautoencoder.MSELoss method) (netmap.model.zinbautoencoder.ZINBAutoencoder method) (netmap.model.zinbautoencoder.ZINBLoss method) (netmap.utils.netmap_config.NetmapConfig method)

A

adata_filename (netmap.utils.netmap_config.NetmapConfig attribute) add_cluster_based_candidate_edges() (in module netmap.masking.internal) add_cluster_wise_spearman() (in module netmap.masking.internal) add_clusters_to_adata() (in module netmap.downstream.gene_clustering) add_external_grn() (in module netmap.masking.external) add_genome_information_to_anndata() (in module netmap.masking.external) add_neighbourhood_expression_mask() (in module netmap.masking.internal) add_top_edge_annotation_cluster() (in module netmap.downstream.edge_selection)

add_top_edge_annotation_global() (in module netmap.downstream.edge_selection) aggregate_attributions() (in module netmap.grn.inferrence) aggregate_edges() (in module netmap.downstream.regulon) aggregate_edges_arbitrary() (in module netmap.downstream.regulon) aggregation_strategy (netmap.utils.netmap_config.NetmapConfig attribute) attribution_one_model() (in module netmap.grn.inferrence) attribution_one_target() (in module netmap.grn.inferrence) attribution_to_anndata() (in module netmap.utils.data_utils) Autoencoder (class in netmap.model.standardautoencoder)

B

binarize_adata() (in module netmap.masking.internal)

C

calculate_jaccard_scores() (in module netmap.downstream.markers) chunked_argsort() (in module netmap.downstream.edge_selection) compute_loss() (netmap.model.nbautoencoder.NegativeBinomialAutoencoder method) (netmap.model.standardautoencoder.Autoencoder method) (netmap.model.zinbautoencoder.ZINBAutoencoder method)

compute_regression() (in module netmap.downstream.gene_clustering) compute_signatures_UCell_scores() (in module netmap.downstream.regulon) create_model_zoo() (in module netmap.model.train_model) create_output_directory() (in module netmap.utils.data_utils) create_pairwise_binary_mask() (in module netmap.masking.internal)

D

downstream_recipe() (in module netmap.downstream.clustering)

E

epochs (netmap.utils.netmap_config.NetmapConfig attribute)

F

filter_tf_names() (in module netmap.utils.tf_utils) find_consistent_pairs() (in module netmap.masking.internal) forward() (netmap.model.nbautoencoder.NegativeBinomialAutoencoder method) (netmap.model.nbautoencoder.NegativeBinomialLoss method) (netmap.model.standardautoencoder.Autoencoder method) (netmap.model.standardautoencoder.LogCoshLoss method) (netmap.model.standardautoencoder.MSELoss method) (netmap.model.zinbautoencoder.ZINBAutoencoder method) (netmap.model.zinbautoencoder.ZINBLoss method)

G

get_genome_annotation_from_gtf() (in module netmap.masking.external) get_grn_targets() (in module netmap.downstream.markers) get_hierarchical_clustering() (in module netmap.downstream.gene_clustering) get_mus() (in module netmap.model.nbautoencoder) (in module netmap.model.zinbautoencoder) get_mus_grouping() (in module netmap.model.nbautoencoder) (in module netmap.model.zinbautoencoder) get_neighborhood_expression() (in module netmap.masking.internal)

get_overlapping_signatures() (in module netmap.downstream.regulon) get_regulators() (in module netmap.masking.external) get_sourcewise_jaccard_regulons() (in module netmap.downstream.regulon) get_tf_index() (in module netmap.utils.tf_utils) get_thetas() (in module netmap.model.nbautoencoder) (in module netmap.model.zinbautoencoder) get_thetas_grouping() (in module netmap.model.nbautoencoder) (in module netmap.model.zinbautoencoder) grn (netmap.utils.netmap_config.NetmapConfig attribute)

I

inferrence() (in module netmap.grn.inferrence) inferrence_h5py() (in module netmap.grn.inferrence)

inferrence_model_wise() (in module netmap.grn.inferrence) inferrence_model_wise_level() (in module netmap.grn.inferrence) input_data (netmap.utils.netmap_config.NetmapConfig attribute)

J

jaccard_similarity() (in module netmap.downstream.regulon)

L

latent() (netmap.model.nbautoencoder.NegativeBinomialAutoencoder method) (netmap.model.standardautoencoder.Autoencoder method) layer (netmap.utils.netmap_config.NetmapConfig attribute)

learning_rate (netmap.utils.netmap_config.NetmapConfig attribute) load_edge_dict_from_dataframe() (in module netmap.downstream.regulon) load_tf_names() (in module netmap.utils.tf_utils) LogCoshLoss (class in netmap.model.standardautoencoder)

M

make_cluster_regulon_dataframe() (in module netmap.downstream.regulon) make_cluster_regulon_dataframe_directional() (in module netmap.downstream.regulon) make_global_target_similarity_plot() (in module netmap.downstream.regulon) masking_percentage (netmap.utils.netmap_config.NetmapConfig attribute) merge_all_to_obs() (in module netmap.utils.data_utils) model (netmap.utils.netmap_config.NetmapConfig attribute) module netmap.downstream.clustering netmap.downstream.edge_selection netmap.downstream.gene_clustering netmap.downstream.markers netmap.downstream.regulon netmap.grn netmap.grn.inferrence netmap.masking netmap.masking.external netmap.masking.internal netmap.model netmap.model.nbautoencoder netmap.model.standardautoencoder netmap.model.train_model netmap.model.zinbautoencoder netmap.utils netmap.utils.data_utils netmap.utils.misc netmap.utils.netmap_config netmap.utils.tf_utils

MSELoss (class in netmap.model.standardautoencoder)

N

n_models (netmap.utils.netmap_config.NetmapConfig attribute) NegativeBinomialAutoencoder (class in netmap.model.nbautoencoder) NegativeBinomialLoss (class in netmap.model.nbautoencoder) netmap.downstream.clustering module netmap.downstream.edge_selection module netmap.downstream.gene_clustering module netmap.downstream.markers module netmap.downstream.regulon module netmap.grn module netmap.grn.inferrence module netmap.masking module netmap.masking.external module netmap.masking.internal module

netmap.model module netmap.model.nbautoencoder module netmap.model.standardautoencoder module netmap.model.train_model module netmap.model.zinbautoencoder module netmap.utils module netmap.utils.data_utils module netmap.utils.misc module netmap.utils.netmap_config module netmap.utils.tf_utils module NetmapConfig (class in netmap.utils.netmap_config)

O

optimizer (netmap.utils.netmap_config.NetmapConfig attribute)

output_directory (netmap.utils.netmap_config.NetmapConfig attribute)

P

penalize_error (netmap.utils.netmap_config.NetmapConfig attribute) plot_jaccard_comparison() (in module netmap.downstream.markers) plot_regression_and_dendrogram() (in module netmap.downstream.gene_clustering) plot_scatter_plot() (in module netmap.downstream.gene_clustering) prepare_jaccard_analysis_df() (in module netmap.downstream.markers)

preprocess_bed_file() (in module netmap.masking.external) print_every (netmap.utils.netmap_config.NetmapConfig attribute) process() (in module netmap.downstream.clustering) process_cell_edges() (in module netmap.downstream.regulon) process_cell_edges_signed() (in module netmap.downstream.regulon)

R

read_yaml() (netmap.utils.netmap_config.NetmapConfig class method) remove_regulon_columns() (in module netmap.utils.data_utils) remove_Ucell_columns() (in module netmap.utils.data_utils)

retrieve_edges_by_index() (in module netmap.utils.data_utils) retrieve_top_edges() (in module netmap.utils.data_utils) return_grn_adata_to_memory() (in module netmap.grn.inferrence)

S

save_anndata() (in module netmap.utils.data_utils) select_top_edges() (in module netmap.downstream.regulon)

select_top_edges_signed() (in module netmap.downstream.regulon) shuffle_each_column_independently() (in module netmap.grn.inferrence) spectral_clustering() (in module netmap.downstream.clustering)

T

tf_only (netmap.utils.netmap_config.NetmapConfig attribute)

transcription_factors (netmap.utils.netmap_config.NetmapConfig attribute)

U

unify_group_labelling() (in module netmap.downstream.clustering)

V

validation_size (netmap.utils.netmap_config.NetmapConfig attribute)

W

write_config() (in module netmap.utils.misc)

write_yaml() (netmap.utils.netmap_config.NetmapConfig method)

X

xai_method (netmap.utils.netmap_config.NetmapConfig attribute)

Z

ZINBAutoencoder (class in netmap.model.zinbautoencoder)

ZINBLoss (class in netmap.model.zinbautoencoder)