Index A | C | D | E | F | G | H | I | L | M | N | P | Q | R | S | T | U | X A adaptative_source_score() (in module troutpy.tl) adaptative_source_score_optimized() (in module troutpy.tl) add_morphological_metrics() (in module troutpy.pp) aggregate_urna() (in module troutpy.pp) apply_exrnaH_to_cellular_to_create_cellularW() (in module troutpy.pl) assess_diffusion() (in module troutpy.tl) C calculate_heuristic_radius_by_cells() (in module troutpy.tl) calculate_target_cells() (in module troutpy.tl) cell_contacts_with_urna_sources() (in module troutpy.tl) cell_type_contacts() (in module troutpy.pl) celltype_contact_matrix() (in module troutpy.pl) (in module troutpy.tl) cluster_distribution_from_source() (in module troutpy.tl) colocalization_proportion() (in module troutpy.tl) communication_strength() (in module troutpy.tl) compare_intra_extra_distribution() (in module troutpy.tl) compute_contribution_score() (in module troutpy.tl) compute_extracellular_counts() (in module troutpy.pp) compute_js_divergence() (in module troutpy.tl) compute_target_score() (in module troutpy.tl) cosmx_converter() (in module troutpy.pp) coupled_scatter() (in module troutpy.pl) create_grid_squares() (in module troutpy.pp) create_urna_metadata() (in module troutpy.tl) crosstab() (in module troutpy.pl) D define_target_by_celltype() (in module troutpy.tl) define_urna() (in module troutpy.pp) define_urna_probability() (in module troutpy.pp) define_urna_probability_stainings() (in module troutpy.pp) density_similarity() (in module troutpy.tl) diffusion_results() (in module troutpy.pl) distributions_by_cluster() (in module troutpy.pl) E extracellular_enrichment() (in module troutpy.tl) F factors_in_cells() (in module troutpy.pl) factors_to_cells() (in module troutpy.tl) filter_urna() (in module troutpy.pp) find_optimal_segmentation_free_bin_size() (in module troutpy.pp) format_adata() (in module troutpy.pp) G gene_communication() (in module troutpy.pl) gene_distribution_from_source() (in module troutpy.pl) gene_metric_heatmap() (in module troutpy.pl) gene_specific_interactions() (in module troutpy.tl) genes_over_noise() (in module troutpy.pl) get_colormap() (in module troutpy.pl) get_gene_interaction_strength() (in module troutpy.tl) get_palette() (in module troutpy.pl) get_proportion_expressed_per_cell_type() (in module troutpy.tl) get_transcript_categories() (in module troutpy.pp) global_distribution_from_source() (in module troutpy.pl) H heatmap() (in module troutpy.pl) histogram() (in module troutpy.pl) I identify_density_k_neighbors() (in module troutpy.tl) image_intensities_per_transcript() (in module troutpy.tl) in_out_correlation() (in module troutpy.tl) interactions_with_arrows() (in module troutpy.pl) intra_extra_density() (in module troutpy.pl) L latent_factor() (in module troutpy.tl) logfoldratio_over_noise() (in module troutpy.pl) M metric_scatter() (in module troutpy.pl) module troutpy.pl troutpy.pp troutpy.tl moranI_histogram() (in module troutpy.pl) N nmf_factors_exrna_cells_W() (in module troutpy.pl) nmf_gene_contributions() (in module troutpy.pl) P paired_nmf_factors() (in module troutpy.pl) pie() (in module troutpy.pl) point_metric_comparison() (in module troutpy.pl) Q quantify_overexpression() (in module troutpy.tl) R rank_factor_genes_loadings() (in module troutpy.pl) rank_factor_genes_loadings_matrixplot() (in module troutpy.pl) S segment_protrusions() (in module troutpy.tl) segmentation_free_clustering() (in module troutpy.tl) segmentation_free_sainsc() (in module troutpy.pp) sorted_heatmap() (in module troutpy.pl) source_score_by_celltype() (in module troutpy.pl) spatial_colocalization() (in module troutpy.tl) spatial_inout_expression() (in module troutpy.pl) spatial_interactions() (in module troutpy.pl) spatial_transcripts() (in module troutpy.pl) spatial_transcripts_source() (in module troutpy.pl) spatial_variability() (in module troutpy.tl) T target_score_by_celltype() (in module troutpy.pl) top_bottom_probes() (in module troutpy.pl) troutpy.pl module troutpy.pp module troutpy.tl module U urna_vs_source_score() (in module troutpy.pl) X xenium_converter() (in module troutpy.pp)