Index _ | A | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U _ __init__() (peach.tl.SearchConfig method) __post_init__() (peach.tl.SearchConfig method), [1] _search_inflation (peach.tl.SearchConfig attribute), [1] A archetypal_coordinates() (in module peach.tl), [1] (in module peach.tl.archetypal) archetypal_space() (in module peach.pl), [1] (in module peach.pl.archetypal) archetypal_space_multi() (in module peach.pl), [1] (in module peach.pl.archetypal) archetype_co_occurrence() (in module peach.tl) (in module peach.tl.spatial) archetype_exclusive_patterns() (in module peach.tl), [1] (in module peach.tl.statistical) archetype_interaction_boundaries() (in module peach.tl) (in module peach.tl.spatial) archetype_nhood_enrichment() (in module peach.tl) (in module peach.tl.spatial) archetype_positions() (in module peach.pl), [1] (in module peach.pl.archetypal) archetype_positions_3d() (in module peach.pl), [1] (in module peach.pl.archetypal) archetype_spatial_autocorr() (in module peach.tl) (in module peach.tl.spatial) archetype_statistics() (in module peach.pl), [1] (in module peach.pl.archetypal) assign_archetypes() (in module peach.tl), [1] (in module peach.tl.archetypal) assign_to_centroids() (in module peach.tl), [1] (in module peach.tl.archetypal) C check_matplotlib_setup() (in module peach.pl.debug_dotplot) co_occurrence() (in module peach.pl) (in module peach.pl.spatial) compute_conditional_centroids() (in module peach.tl), [1] (in module peach.tl.archetypal) compute_lineage_drivers() (in module peach.tl), [1] (in module peach.tl.cellrank_integration) compute_lineage_pseudotimes() (in module peach.tl), [1] (in module peach.tl.cellrank_integration) compute_pathway_scores() (in module peach.pp), [1] (in module peach.pp.basic) compute_transition_frequencies() (in module peach.tl), [1] (in module peach.tl.cellrank_integration) conditional_associations() (in module peach.tl), [1] (in module peach.tl.statistical) cross_correlations() (in module peach.pl) (in module peach.pl.spatial) cv_folds (peach.tl.SearchConfig attribute), [1] D debug_dotplot() (in module peach.pl.debug_dotplot) dotplot() (in module peach.pl), [1] (in module peach.pl.results) E early_stopping_patience (peach.tl.SearchConfig attribute), [1] elbow_curve() (in module peach.pl), [1] (in module peach.pl.archetypal) extract_archetype_weights() (in module peach.tl), [1] (in module peach.tl.archetypal) F fate_probabilities() (in module peach.pl), [1] (in module peach.pl.cellrank_viz) G gene_associations() (in module peach.tl), [1] (in module peach.tl.statistical) gene_trends() (in module peach.pl.cellrank_viz) generate_synthetic() (in module peach.pp), [1] (in module peach.pp.basic) H hidden_dims_options (peach.tl.SearchConfig attribute), [1] hyperparameter_search() (in module peach.tl), [1] (in module peach.tl.hyperparameters) I inflation_factor_range (peach.tl.SearchConfig attribute), [1] interaction_boundaries() (in module peach.pl) (in module peach.pl.spatial) L lineage_drivers() (in module peach.pl), [1] (in module peach.pl.cellrank_viz) load_data() (in module peach.pp), [1] (in module peach.pp.basic) load_pathway_networks() (in module peach.pp), [1] (in module peach.pp.basic) M max_cells_cv (peach.tl.SearchConfig attribute), [1] max_epochs_cv (peach.tl.SearchConfig attribute), [1] module peach.pl peach.pl.archetypal peach.pl.cellrank_viz peach.pl.debug_dotplot peach.pl.pattern_visualization peach.pl.results peach.pl.spatial peach.pp peach.pp.basic peach.tl peach.tl.archetypal peach.tl.cellrank_integration peach.tl.hyperparameters peach.tl.spatial peach.tl.statistical N n_archetypes_range (peach.tl.SearchConfig attribute), [1] nhood_enrichment() (in module peach.pl) (in module peach.pl.spatial) P pathway_associations() (in module peach.tl), [1] (in module peach.tl.statistical) pattern_analysis() (in module peach.tl), [1] (in module peach.tl.statistical) pattern_dotplot() (in module peach.pl), [1] (in module peach.pl.pattern_visualization) pattern_heatmap() (in module peach.pl), [1] (in module peach.pl.pattern_visualization) pattern_summary_barplot() (in module peach.pl), [1] (in module peach.pl.pattern_visualization) peach.pl module peach.pl.archetypal module peach.pl.cellrank_viz module peach.pl.debug_dotplot module peach.pl.pattern_visualization module peach.pl.results module peach.pl.spatial module peach.pp module peach.pp.basic module peach.tl module peach.tl.archetypal module peach.tl.cellrank_integration module peach.tl.hyperparameters module peach.tl.spatial module peach.tl.statistical module prepare_atacseq() (in module peach.pp) (in module peach.pp.basic) prepare_training() (in module peach.pp), [1] (in module peach.pp.basic) R random_state (peach.tl.SearchConfig attribute), [1] S SearchConfig (class in peach.tl), [1] setup_cellrank() (in module peach.tl), [1] (in module peach.tl.cellrank_integration) single_trajectory_analysis() (in module peach.tl), [1] (in module peach.tl.cellrank_integration) spatial_archetypes() (in module peach.pl) (in module peach.pl.spatial) spatial_autocorr() (in module peach.pl) (in module peach.pl.spatial) spatial_neighbors() (in module peach.tl) (in module peach.tl.spatial) specialization_patterns() (in module peach.tl), [1] (in module peach.tl.statistical) speed_preset (peach.tl.SearchConfig attribute), [1] subsample_fraction (peach.tl.SearchConfig attribute), [1] T tradeoff_patterns() (in module peach.tl), [1] (in module peach.tl.statistical) train_archetypal() (in module peach.tl), [1] (in module peach.tl.archetypal) training_metrics() (in module peach.pl), [1] (in module peach.pl.archetypal) U use_pcha_init (peach.tl.SearchConfig attribute), [1]