Index

A

add_deconvolution_results_to_dataset() (in module bayestme.deconvolution) add_logging_args() (in module bayestme.log_config) add_marker_gene_results_to_dataset() (in module bayestme.deconvolution)

adjacency_matrix_from_edges() (in module bayestme.communities) align_celltype() (bayestme.data.DeconvolutionResult method) align_clusters() (in module bayestme.communities)

B

backward_sample() (bayestme.hmm_fast.HMM method) bayestme.bleeding_correction module bayestme.communities module bayestme.cv_likelihoods module bayestme.data module bayestme.deconvolution module bayestme.expression_truth module bayestme.fast_multivariate_normal module bayestme.gene_filtering module bayestme.gfbt_multinomial module

bayestme.hmm_fast module bayestme.log_config module bayestme.model_bkg module bayestme.phenotype_selection module bayestme.plotting module bayestme.semi_synthetic_spatial module bayestme.spatial_expression module bayestme.synthetic_data module bayestme.utils module BleedCorrectionResult (class in bayestme.data) build_basis_indices() (in module bayestme.bleeding_correction)

C

calculate_pairwise_coordinate_differences() (in module bayestme.bleeding_correction) calculate_probs() (bayestme.gfbt_multinomial.GraphFusedBinomialTree method) calculate_spatial_genes() (in module bayestme.spatial_expression) cell_type_counts (bayestme.data.SpatialExpressionDataset property) cell_type_probabilities (bayestme.data.SpatialExpressionDataset property) checkpoint_variable_state() (bayestme.spatial_expression.SpatialDifferentialExpression method) clean_bleed() (in module bayestme.bleeding_correction) clear_checkpoint() (bayestme.spatial_expression.SpatialDifferentialExpression method) combine_multiple_expression_truth() (in module bayestme.expression_truth) communities_from_posteriors() (in module bayestme.communities)

communities_from_posteriors_separate() (in module bayestme.communities) configure_logging() (in module bayestme.log_config) constant_state (bayestme.spatial_expression.SpatialDifferentialExpression attribute) construct_composite_trendfilter() (in module bayestme.utils) construct_edge_adjacency() (in module bayestme.utils) construct_trendfilter() (in module bayestme.utils) counts_from_outcomes() (bayestme.gfbt_multinomial.GraphFusedBinomialTree method) create_anndata_object() (in module bayestme.data) create_folds() (in module bayestme.phenotype_selection) create_top_gene_lists() (in module bayestme.deconvolution) create_top_n_gene_bleeding_plots() (in module bayestme.bleeding_correction)

D

decontaminate_spots() (in module bayestme.bleeding_correction) DeconvolutionResult (class in bayestme.data)

deconvolve() (in module bayestme.deconvolution) dirichlet_alpha_model() (in module bayestme.expression_truth)

E

edges (bayestme.data.SpatialExpressionDataset property)

emission_fast() (in module bayestme.hmm_fast) exhaustive_best_permutation() (in module bayestme.communities)

F

FALSE_DISCOVERY_RATE (bayestme.deconvolution.MarkerGeneMethod attribute) ffbs() (bayestme.hmm_fast.HMM method) filter_disconnected_points() (in module bayestme.spatial_expression) filter_genes_by_spot_threshold() (in module bayestme.gene_filtering) filter_list_of_genes() (in module bayestme.gene_filtering) filter_pseudogenes_from_selection() (in module bayestme.spatial_expression) filter_reads_to_top_n_genes() (in module bayestme.utils)

filter_ribosome_genes() (in module bayestme.gene_filtering) filter_stdata_to_match_expression_truth() (in module bayestme.gene_filtering) FilterType (class in bayestme.gene_filtering) fit_alpha_for_multiple_samples() (in module bayestme.expression_truth) fit_basis_functions() (in module bayestme.bleeding_correction) fit_spot_rates() (in module bayestme.bleeding_correction) forward_filter() (bayestme.hmm_fast.HMM method) from_arrays() (bayestme.data.SpatialExpressionDataset class method)

G

gaussian_aicc() (in module bayestme.communities) gaussian_aicc_bic_mixture() (in module bayestme.communities) gaussian_bic() (in module bayestme.communities) gene_names (bayestme.data.SpatialExpressionDataset property) generate_demo_dataset() (in module bayestme.synthetic_data) generate_fake_stdataset() (in module bayestme.synthetic_data) generate_semi_synthetic() (in module bayestme.semi_synthetic_spatial) generate_simulated_bleeding_reads_data() (in module bayestme.synthetic_data) get_best_lambda_value() (in module bayestme.cv_likelihoods) get_edges() (in module bayestme.utils) get_kth_order_discrete_difference_operator() (in module bayestme.utils) get_max_likelihood_n_components() (in module bayestme.cv_likelihoods) get_n_cell_correlation() (in module bayestme.spatial_expression)

get_n_neighbors() (in module bayestme.phenotype_selection) get_phenotype_selection_parameters_for_folds() (in module bayestme.phenotype_selection) get_posmap() (in module bayestme.utils) get_proportion_of_spots_in_k_with_pattern_h_per_gene() (in module bayestme.spatial_expression) get_rank() (in module bayestme.semi_synthetic_spatial) get_state() (bayestme.spatial_expression.SpatialDifferentialExpression method) get_stddev_ordering() (in module bayestme.utils) get_suggested_initial_local_weight() (in module bayestme.bleeding_correction) get_top_gene_names_by_stddev() (in module bayestme.utils) get_wedge_dimensions_from_value_array() (in module bayestme.plotting) get_x_y_arrays_for_layout() (in module bayestme.plotting) GraphFusedBinomialTree (class in bayestme.gfbt_multinomial) GraphFusedMultinomial (class in bayestme.model_bkg) greedy_best_permutation() (in module bayestme.communities)

H

has_non_tissue_spots() (in module bayestme.bleeding_correction)

HEX (bayestme.data.Layout attribute) HMM (class in bayestme.hmm_fast)

I

ilogit() (in module bayestme.utils) imshow_matrix() (in module bayestme.bleeding_correction) initialize() (bayestme.spatial_expression.SpatialDifferentialExpression method)

is_csv() (in module bayestme.data) is_csv_tsv() (in module bayestme.data) is_first_order_discrete_difference_operator() (in module bayestme.utils) is_tsv() (in module bayestme.data)

L

layout (bayestme.data.SpatialExpressionDataset property) Layout (class in bayestme.data) load_expression_truth() (in module bayestme.expression_truth) load_from_state() (bayestme.spatial_expression.SpatialDifferentialExpression class method)

load_likelihoods() (in module bayestme.cv_likelihoods) load_model() (bayestme.model_bkg.GraphFusedMultinomial method) log_likelihood() (in module bayestme.utils) logp() (in module bayestme.utils)

M

marker_gene_indices (bayestme.data.SpatialExpressionDataset property) marker_gene_names (bayestme.data.SpatialExpressionDataset property) MarkerGeneMethod (class in bayestme.deconvolution) module bayestme.bleeding_correction bayestme.communities bayestme.cv_likelihoods bayestme.data bayestme.deconvolution bayestme.expression_truth bayestme.fast_multivariate_normal bayestme.gene_filtering bayestme.gfbt_multinomial bayestme.hmm_fast bayestme.log_config bayestme.model_bkg bayestme.phenotype_selection bayestme.plotting bayestme.semi_synthetic_spatial bayestme.spatial_expression bayestme.synthetic_data bayestme.utils

moran_i() (in module bayestme.spatial_expression) multinomial_rvs() (in module bayestme.utils)

N

n_cell_types (bayestme.data.SpatialExpressionDataset property) n_components (bayestme.data.SpatialDifferentialExpressionResult property) n_gene (bayestme.data.SpatialExpressionDataset property)

n_spatial_patterns (bayestme.data.SpatialDifferentialExpressionResult property) n_spot (bayestme.data.SpatialExpressionDataset property) n_spot_in (bayestme.data.SpatialExpressionDataset property)

O

omega (bayestme.data.DeconvolutionResult property) omega_difference (bayestme.data.DeconvolutionResult property) (bayestme.data.SpatialExpressionDataset property)

order_reads_by_stddev() (in module bayestme.utils)

P

PhenotypeSelectionResult (class in bayestme.data) plot_basis_functions() (in module bayestme.bleeding_correction) plot_before_after_cleanup() (in module bayestme.bleeding_correction) plot_bleed_vectors() (in module bayestme.bleeding_correction) plot_bleeding() (in module bayestme.bleeding_correction) plot_cell_num() (in module bayestme.deconvolution) plot_cell_num_scatterpie() (in module bayestme.deconvolution) plot_cell_prob() (in module bayestme.deconvolution) plot_colored_spatial_polygon() (in module bayestme.plotting) plot_cv_running() (in module bayestme.cv_likelihoods) plot_deconvolution() (in module bayestme.deconvolution) plot_folds() (in module bayestme.phenotype_selection)

plot_gene_in_tissue_counts() (in module bayestme.plotting) plot_gene_raw_counts() (in module bayestme.plotting) plot_likelihoods() (in module bayestme.cv_likelihoods) plot_marker_genes() (in module bayestme.deconvolution) plot_significant_spatial_patterns() (in module bayestme.spatial_expression) plot_spatial_pattern() (in module bayestme.spatial_expression) plot_spatial_pattern_and_all_constituent_genes() (in module bayestme.spatial_expression) plot_spatial_pattern_legend() (in module bayestme.spatial_expression) plot_spatial_pattern_with_legend() (in module bayestme.spatial_expression) plot_spatial_pie_charts() (in module bayestme.plotting) positions (bayestme.data.SpatialExpressionDataset property) positions_tissue (bayestme.data.SpatialExpressionDataset property)

R

rates_from_raw() (in module bayestme.bleeding_correction) raw_counts (bayestme.data.SpatialExpressionDataset property) read_count_mat() (bayestme.data.SpatialExpressionDataset class method) read_h5() (bayestme.data.BleedCorrectionResult class method) (bayestme.data.DeconvolutionResult class method) (bayestme.data.PhenotypeSelectionResult class method) (bayestme.data.SpatialDifferentialExpressionResult class method) (bayestme.data.SpatialDifferentialExpressionSamplerState class method) (bayestme.data.SpatialExpressionDataset class method)

read_legacy_h5() (bayestme.data.SpatialExpressionDataset class method) read_spaceranger() (bayestme.data.SpatialExpressionDataset class method) reads (bayestme.data.SpatialExpressionDataset property) relative_expression (bayestme.data.DeconvolutionResult property) resample() (bayestme.gfbt_multinomial.GraphFusedBinomialTree method) reset_to_checkpoint() (bayestme.spatial_expression.SpatialDifferentialExpression method) RIBOSOME (bayestme.gene_filtering.FilterType attribute) run_phenotype_selection_single_job() (in module bayestme.phenotype_selection) run_spatial_expression() (in module bayestme.spatial_expression)

S

sample() (bayestme.model_bkg.GraphFusedMultinomial method) (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_beta() (bayestme.model_bkg.GraphFusedMultinomial method) sample_cell_num() (bayestme.model_bkg.GraphFusedMultinomial method) sample_graph_fused_multinomial() (in module bayestme.phenotype_selection) sample_horseshoe_plus() (in module bayestme.utils) sample_multivariate_normal() (in module bayestme.fast_multivariate_normal) sample_multivariate_normal_from_covariance() (in module bayestme.fast_multivariate_normal) sample_multivariate_normal_from_precision() (in module bayestme.fast_multivariate_normal) sample_pattern_probs() (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_pg() (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_phi() (bayestme.model_bkg.GraphFusedMultinomial method) sample_probs() (bayestme.model_bkg.GraphFusedMultinomial method) sample_reads() (bayestme.model_bkg.GraphFusedMultinomial method) sample_sigmainv() (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_spatial_assignments() (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_spatial_patterns() (bayestme.spatial_expression.SpatialDifferentialExpression method) sample_spatial_weights() (bayestme.spatial_expression.SpatialDifferentialExpression method) save() (bayestme.data.BleedCorrectionResult method) (bayestme.data.DeconvolutionResult method) (bayestme.data.PhenotypeSelectionResult method) (bayestme.data.SpatialDifferentialExpressionResult method) (bayestme.data.SpatialDifferentialExpressionSamplerState method) (bayestme.data.SpatialExpressionDataset method)

save_model() (bayestme.model_bkg.GraphFusedMultinomial method) select_local_weight() (in module bayestme.bleeding_correction) select_marker_genes() (in module bayestme.deconvolution) select_significant_spatial_programs() (in module bayestme.spatial_expression) select_top_genes_by_standard_deviation() (in module bayestme.gene_filtering) ship_up() (bayestme.hmm_fast.HMM method) softplus() (in module bayestme.bleeding_correction) spatial_detection() (bayestme.spatial_expression.SpatialDifferentialExpression method) SpatialDifferentialExpression (class in bayestme.spatial_expression) SpatialDifferentialExpressionResult (class in bayestme.data) SpatialDifferentialExpressionSamplerState (class in bayestme.data) SpatialExpressionDataset (class in bayestme.data) SPOTS (bayestme.gene_filtering.FilterType attribute) SQUARE (bayestme.data.Layout attribute) stable_softmax() (in module bayestme.utils) swap_labels() (in module bayestme.communities)

T

test_communities() (in module bayestme.communities) TIGHT (bayestme.deconvolution.MarkerGeneMethod attribute) tissue_mask (bayestme.data.SpatialExpressionDataset property)

tissue_mask_to_grid() (in module bayestme.bleeding_correction) transition_mat() (in module bayestme.model_bkg) transition_mat_vec() (in module bayestme.hmm_fast)

V

variable_state (bayestme.spatial_expression.SpatialDifferentialExpression attribute)

W

weights_from_basis() (in module bayestme.bleeding_correction)