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Netmap 0.1 documentation
Netmap 0.1 documentation

API Reference

  • API Reference
    • netmap
      • netmap.downstream
        • netmap.downstream.clustering
          • netmap.downstream.clustering.downstream_recipe
          • netmap.downstream.clustering.process
          • netmap.downstream.clustering.spectral_clustering
          • netmap.downstream.clustering.unify_group_labelling
        • netmap.downstream.edge_selection
          • netmap.downstream.edge_selection.add_top_edge_annotation_cluster
          • netmap.downstream.edge_selection.add_top_edge_annotation_global
          • netmap.downstream.edge_selection.chunked_argsort
        • netmap.downstream.final_downstream
          • netmap.downstream.final_downstream.compute_edge_overlaps_simple
          • netmap.downstream.final_downstream.create_regulon_activity_adata
          • netmap.downstream.final_downstream.curate_network
          • netmap.downstream.final_downstream.filter_clusters_by_cell_count
          • netmap.downstream.final_downstream.filter_grn_by_top_signatures
          • netmap.downstream.final_downstream.filter_signatures_by_Ucell
          • netmap.downstream.final_downstream.get_top_targets
          • netmap.downstream.final_downstream.plot_reg
          • netmap.downstream.final_downstream.plot_reg_curated
          • netmap.downstream.final_downstream.plot_shared_targets_heatmap
        • netmap.downstream.gene_clustering
          • netmap.downstream.gene_clustering.add_clusters_to_adata
          • netmap.downstream.gene_clustering.compute_regression
          • netmap.downstream.gene_clustering.get_hierarchical_clustering
          • netmap.downstream.gene_clustering.plot_regression_and_dendrogram
          • netmap.downstream.gene_clustering.plot_scatter_plot
        • netmap.downstream.plotting
      • netmap.masking
        • netmap.masking.external
          • netmap.masking.external.add_external_grn
          • netmap.masking.external.add_genome_information_to_anndata
          • netmap.masking.external.get_genome_annotation_from_gtf
          • netmap.masking.external.get_regulators
          • netmap.masking.external.preprocess_bed_file
        • netmap.masking.internal
          • netmap.masking.internal.add_neighbourhood_expression_mask
          • netmap.masking.internal.binarize_adata
          • netmap.masking.internal.create_pairwise_binary_mask
          • netmap.masking.internal.find_consistent_pairs
          • netmap.masking.internal.get_neighborhood_expression
      • netmap.model
        • netmap.model.nbautoencoder
          • netmap.model.nbautoencoder.get_mus
          • netmap.model.nbautoencoder.get_mus_grouping
          • netmap.model.nbautoencoder.get_thetas
          • netmap.model.nbautoencoder.get_thetas_grouping
          • netmap.model.nbautoencoder.NegativeBinomialAutoencoder
          • netmap.model.nbautoencoder.NegativeBinomialLoss
        • netmap.model.standardautoencoder
          • netmap.model.standardautoencoder.Autoencoder
          • netmap.model.standardautoencoder.LogCoshLoss
          • netmap.model.standardautoencoder.MSELoss
        • netmap.model.train_model
          • netmap.model.train_model.create_model_zoo
        • netmap.model.zinbautoencoder
          • netmap.model.zinbautoencoder.get_mus
          • netmap.model.zinbautoencoder.get_mus_grouping
          • netmap.model.zinbautoencoder.get_thetas
          • netmap.model.zinbautoencoder.get_thetas_grouping
          • netmap.model.zinbautoencoder.ZINBAutoencoder
          • netmap.model.zinbautoencoder.ZINBLoss
      • netmap.utils
        • netmap.utils.data_utils
          • netmap.utils.data_utils.attribution_to_anndata
          • netmap.utils.data_utils.create_output_directory
          • netmap.utils.data_utils.merge_all_to_obs
          • netmap.utils.data_utils.remove_regulon_columns
          • netmap.utils.data_utils.retrieve_edges_by_column
          • netmap.utils.data_utils.retrieve_top_edges
          • netmap.utils.data_utils.save_anndata
        • netmap.utils.misc
          • netmap.utils.misc.write_config
        • netmap.utils.netmap_config
          • netmap.utils.netmap_config.NetmapConfig
        • netmap.utils.tf_utils
          • netmap.utils.tf_utils.filter_tf_names
          • netmap.utils.tf_utils.get_tf_index
          • netmap.utils.tf_utils.load_tf_names
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NetmapConfig

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