Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | V | W A all_embeddings() (in module popari.pl) annotate_domain() (popari.simulation_framework.SyntheticDataset method) annotate_replicate_domain() (popari.simulation_framework.MultiReplicateSyntheticDataset method) annotation_mode (popari.simulation_framework.SimulationParameters attribute) assign_domain_labels() (popari.simulation_framework.MultiReplicateSyntheticDataset method) (popari.simulation_framework.SyntheticDataset method) B betas (popari.model.Popari attribute) binning_downsample_rate (popari.model.Popari attribute) C calculate_neighbors() (popari.simulation_framework.MultiReplicateSyntheticDataset method) cell_type_definitions (popari.simulation_framework.SimulationParameters attribute) clusters_to_categories() (in module popari.pl) compute_ari_scores() (in module popari.tl) compute_columnwise_autocorrelation() (in module popari.tl) compute_confusion_matrix() (in module popari.tl) compute_empirical_correlations() (in module popari.tl) compute_silhouette_scores() (in module popari.tl) compute_spatial_neighbors() (popari.components.PopariDataset method) confusion_matrix() (in module popari.pl) coordinates_key (popari.components.PopariDataset attribute) D dataset (popari.components.PopariDataset attribute) dataset_path (popari.model.Popari attribute) datasets (popari.model.Popari attribute) domain_key (popari.simulation_framework.SimulationParameters attribute) E embedding_acceleration_trick (popari.model.Popari attribute) embedding_mini_iterations (popari.model.Popari attribute) embedding_step_size_multiplier (popari.model.Popari attribute) estimate_parameters() (popari.model.Popari method) estimate_weights() (popari.model.Popari method) evaluate_classification_task() (in module popari.tl) F find_differential_genes() (in module popari.tl) G grid_size (popari.simulation_framework.SimulationParameters attribute) H height (popari.simulation_framework.SimulationParameters attribute) hierarchical_levels (popari.model.Popari attribute) I in_situ() (in module popari.pl) initial_context (popari.model.Popari attribute) initialization_method (popari.model.Popari attribute) K K (popari.model.Popari attribute) L lambda_M (popari.model.Popari attribute) lambda_s (popari.simulation_framework.SimulationParameters attribute) lambda_Sigma_bar (popari.model.Popari attribute) lambda_Sigma_x_inv (popari.model.Popari attribute) leiden() (in module popari.tl) load_anndata() (in module popari.io) load_anndata_datasets() (popari.model.Popari method) load_dataset() (popari.model.Popari method) load_trained_model() (in module popari.model) M M_constraint (popari.model.Popari attribute) metagene_embedding() (in module popari.pl) metagene_groups (popari.model.Popari attribute) metagene_gsea() (in module popari.tl) metagene_mode (popari.model.Popari attribute) metagene_signature_enrichment() (in module popari.pl) metagene_variation_probabilities (popari.simulation_framework.SimulationParameters attribute) minimum_distance (popari.simulation_framework.SimulationParameters attribute) module popari popari.components popari.io popari.model popari.pl popari.simulation_framework popari.tl multigroup_heatmap() (in module popari.pl) multireplicate_heatmap() (in module popari.pl) MultiReplicateSyntheticDataset (class in popari.simulation_framework) N nll() (popari.model.Popari method) noise_metagene_parameter (popari.simulation_framework.SimulationParameters attribute) num_cells (popari.simulation_framework.SimulationParameters attribute) num_genes (popari.simulation_framework.SimulationParameters attribute) num_noise_metagenes (popari.simulation_framework.SimulationParameters attribute) num_real_metagenes (popari.simulation_framework.SimulationParameters attribute) P plot_gene_activations() (in module popari.tl) plot_gene_trajectories() (in module popari.tl) plot_metagene_embedding() (popari.components.PopariDataset method) popari module Popari (class in popari.model) popari.components module popari.io module popari.model module popari.pl module popari.simulation_framework module popari.tl module PopariDataset (class in popari.components) preprocess_embeddings() (in module popari.tl) pretrained (popari.model.Popari attribute) prior_x_modes (popari.model.Popari attribute) propagate_labels() (in module popari.tl) R random_state (popari.model.Popari attribute) real_metagene_parameter (popari.simulation_framework.SimulationParameters attribute) reloaded_hierarchy (popari.model.Popari attribute) remove_connectivity_artifacts() (popari.components.PopariDataset static method) replicate_name (popari.components.PopariDataset attribute) replicate_names (popari.model.Popari attribute) S sample_noisy_expression() (popari.simulation_framework.SyntheticDataset method) save_anndata() (in module popari.io) save_results() (popari.model.Popari method) set_superresolution_lr() (popari.model.Popari method) sig_x_scale (popari.simulation_framework.SimulationParameters attribute) sig_y_scale (popari.simulation_framework.SimulationParameters attribute) sigma_yx_inv_mode (popari.model.Popari attribute) simulate_expression() (popari.simulation_framework.MultiReplicateSyntheticDataset method) (popari.simulation_framework.SyntheticDataset method) simulate_metagene_based_expression() (popari.simulation_framework.SyntheticDataset method) simulate_nsf_expression() (popari.simulation_framework.SyntheticDataset method) SimulationParameters (class in popari.simulation_framework) spatial_affinity_centering (popari.model.Popari attribute) spatial_affinity_constraint (popari.model.Popari attribute) spatial_affinity_groups (popari.model.Popari attribute) spatial_affinity_lr (popari.model.Popari attribute) spatial_affinity_mode (popari.model.Popari attribute) spatial_affinity_regularization_power (popari.model.Popari attribute) spatial_affinity_scaling (popari.model.Popari attribute) spatial_affinity_tol (popari.model.Popari attribute) spatial_distributions (popari.simulation_framework.SimulationParameters attribute) superresolution_lr (popari.model.Popari attribute) superresolve() (popari.model.Popari method) synchronize_datasets() (popari.model.Popari method) synthesize_cell_embeddings() (popari.simulation_framework.SyntheticDataset method) synthesize_metagenes() (popari.simulation_framework.SyntheticDataset method) SyntheticDataset (class in popari.simulation_framework) T torch_context (popari.model.Popari attribute) U use_inplace_ops (popari.model.Popari attribute) V verbose (popari.model.Popari attribute) W width (popari.simulation_framework.SimulationParameters attribute)