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Netmap 0.1 documentation
Netmap 0.1 documentation

Tutorials

  • Tutorials

API Reference

  • API Reference
    • 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.grn
      • netmap.grn.inferrence
        • netmap.grn.inferrence.aggregate_attributions
        • netmap.grn.inferrence.attribution_one_model
        • netmap.grn.inferrence.attribution_one_target
        • netmap.grn.inferrence.inferrence
        • netmap.grn.inferrence.inferrence_h5py
        • netmap.grn.inferrence.inferrence_model_wise
        • netmap.grn.inferrence.inferrence_model_wise_level
        • netmap.grn.inferrence.return_grn_adata_to_memory
        • netmap.grn.inferrence.shuffle_each_column_independently
    • 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_cluster_based_candidate_edges
        • netmap.masking.internal.add_cluster_wise_spearman
        • 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.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.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.markers
      • netmap.downstream.markers.calculate_jaccard_scores
      • netmap.downstream.markers.get_grn_targets
      • netmap.downstream.markers.plot_jaccard_comparison
      • netmap.downstream.markers.prepare_jaccard_analysis_df
    • netmap.downstream.regulon
      • netmap.downstream.regulon.aggregate_edges
      • netmap.downstream.regulon.aggregate_edges_arbitrary
      • netmap.downstream.regulon.compute_signatures_UCell_scores
      • netmap.downstream.regulon.get_overlapping_signatures
      • netmap.downstream.regulon.get_sourcewise_jaccard_regulons
      • netmap.downstream.regulon.jaccard_similarity
      • netmap.downstream.regulon.load_edge_dict_from_dataframe
      • netmap.downstream.regulon.make_cluster_regulon_dataframe
      • netmap.downstream.regulon.make_cluster_regulon_dataframe_directional
      • netmap.downstream.regulon.make_global_target_similarity_plot
      • netmap.downstream.regulon.process_cell_edges
      • netmap.downstream.regulon.process_cell_edges_signed
      • netmap.downstream.regulon.select_top_edges
      • netmap.downstream.regulon.select_top_edges_signed
    • 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_Ucell_columns
        • netmap.utils.data_utils.remove_regulon_columns
        • netmap.utils.data_utils.retrieve_edges_by_index
        • 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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