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

add_clusters_to_adata() (in module netmap.downstream.gene_clustering) add_external_grn() (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) attribution_to_anndata() (in module netmap.utils.data_utils) Autoencoder (class in netmap.model.standardautoencoder)

C

compute_edge_overlaps_simple() (in module netmap.downstream.final_downstream) compute_regression() (in module netmap.downstream.gene_clustering) 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) create_regulon_activity_adata() (in module netmap.downstream.final_downstream) curate_network() (in module netmap.downstream.final_downstream)

D

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

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

F

filter_clusters_by_cell_count() (in module netmap.downstream.final_downstream) filter_grn_by_top_signatures() (in module netmap.downstream.final_downstream)

filter_signatures_by_Ucell() (in module netmap.downstream.final_downstream) filter_tf_names() (in module netmap.utils.tf_utils) find_consistent_pairs() (in module netmap.masking.internal)

G

get_genome_annotation_from_gtf() (in module netmap.masking.external) 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_regulators() (in module netmap.masking.external) 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) get_top_targets() (in module netmap.downstream.final_downstream)

L

load_tf_names() (in module netmap.utils.tf_utils)

LogCoshLoss (class in netmap.model.standardautoencoder)

M

module netmap netmap.downstream netmap.downstream.clustering netmap.downstream.edge_selection netmap.downstream.final_downstream netmap.downstream.gene_clustering 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

NegativeBinomialAutoencoder (class in netmap.model.nbautoencoder) NegativeBinomialLoss (class in netmap.model.nbautoencoder) netmap module netmap.downstream module netmap.downstream.clustering module netmap.downstream.edge_selection module netmap.downstream.final_downstream module netmap.downstream.gene_clustering 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)

P

plot_reg() (in module netmap.downstream.final_downstream) plot_reg_curated() (in module netmap.downstream.final_downstream) plot_regression_and_dendrogram() (in module netmap.downstream.gene_clustering)

plot_scatter_plot() (in module netmap.downstream.gene_clustering) plot_shared_targets_heatmap() (in module netmap.downstream.final_downstream) preprocess_bed_file() (in module netmap.masking.external) process() (in module netmap.downstream.clustering)

S

save_anndata() (in module netmap.utils.data_utils)

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

U

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

W

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

Z

ZINBAutoencoder (class in netmap.model.zinbautoencoder)

ZINBLoss (class in netmap.model.zinbautoencoder)