Index

A

add_deconvolution_results_to_dataset() (in module bayestme.data)

add_logging_args() (in module bayestme.log_config) align_celltype() (bayestme.data.DeconvolutionResult method)

B

bayestme.cv_likelihoods module bayestme.data module bayestme.deconvolution module bayestme.expression_truth module bayestme.gene_filtering module bayestme.log_config module

bayestme.semi_synthetic_spatial module bayestme.svi.deconvolution module bayestme.synthetic_data module bayestme.utils module BayesTME_VI (class in bayestme.svi.deconvolution) BleedCorrectionResult (class in bayestme.data)

C

calculate_celltype_profile_prior_from_adata() (in module bayestme.expression_truth) cell_num_trace (bayestme.data.DeconvolutionResult property) cell_type_counts (bayestme.data.SpatialExpressionDataset property) cell_type_probabilities (bayestme.data.SpatialExpressionDataset property) combine_multiple_expression_truth() (in module bayestme.expression_truth) configure_logging() (in module bayestme.log_config) construct_composite_trendfilter() (in module bayestme.utils)

construct_edge_adjacency() (in module bayestme.utils) construct_trendfilter() (in module bayestme.utils) copy() (bayestme.data.SpatialExpressionDataset method) counts (bayestme.data.SpatialExpressionDataset property) create_anndata_object() (in module bayestme.data) create_deconvolve_dataset() (in module bayestme.synthetic_data) create_toy_deconvolve_result() (in module bayestme.synthetic_data)

D

deconvolution() (bayestme.svi.deconvolution.BayesTME_VI method) DeconvolutionResult (class in bayestme.data)

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

E

edges (bayestme.data.SpatialExpressionDataset property)

F

filter_genes_by_spot_threshold() (in module bayestme.gene_filtering) filter_list_of_genes() (in module bayestme.gene_filtering) 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) from_arrays() (bayestme.data.SpatialExpressionDataset class method)

G

gene_names (bayestme.data.SpatialExpressionDataset property) generate_demo_dataset() (in module bayestme.synthetic_data) generate_demo_dataset_with_bleeding() (in module bayestme.synthetic_data) generate_demo_stp_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_knn_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_posmap() (in module bayestme.utils) get_rank() (in module bayestme.semi_synthetic_spatial) get_regular_grid_edges() (in module bayestme.utils) get_stddev_ordering() (in module bayestme.utils) get_top_gene_names_by_stddev() (in module bayestme.utils) guide() (bayestme.svi.deconvolution.BayesTME_VI method)

I

ilogit() (in module bayestme.utils) 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) load_expression_truth() (in module bayestme.expression_truth)

load_likelihoods() (in module bayestme.cv_likelihoods) 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) model() (bayestme.svi.deconvolution.BayesTME_VI method) module bayestme.cv_likelihoods bayestme.data bayestme.deconvolution bayestme.expression_truth bayestme.gene_filtering bayestme.log_config bayestme.semi_synthetic_spatial bayestme.svi.deconvolution bayestme.synthetic_data bayestme.utils

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) nb_probs (bayestme.data.DeconvolutionResult 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_cv_running() (in module bayestme.cv_likelihoods) plot_likelihoods() (in module bayestme.cv_likelihoods)

plot_loss() (bayestme.svi.deconvolution.BayesTME_VI method) positions (bayestme.data.SpatialExpressionDataset property) positions_tissue (bayestme.data.SpatialExpressionDataset property)

R

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.SpatialExpressionDataset class method)

read_spaceranger() (bayestme.data.SpatialExpressionDataset class method) read_with_maybe_header() (in module bayestme.data) reads_trace (bayestme.data.DeconvolutionResult property) relative_expression (bayestme.data.DeconvolutionResult property) relative_mean_expression (bayestme.data.DeconvolutionResult property) (bayestme.data.SpatialExpressionDataset property) RIBOSOME (bayestme.gene_filtering.FilterType attribute) rv_should_be_sampled() (in module bayestme.svi.deconvolution)

S

sample_from_posterior() (in module bayestme.deconvolution) sample_horseshoe_plus() (in module bayestme.utils) save() (bayestme.data.BleedCorrectionResult method) (bayestme.data.DeconvolutionResult method) (bayestme.data.PhenotypeSelectionResult method) (bayestme.data.SpatialDifferentialExpressionResult method) (bayestme.data.SpatialExpressionDataset method)

select_top_genes_by_standard_deviation() (in module bayestme.gene_filtering) spatial_guide() (bayestme.svi.deconvolution.BayesTME_VI method) spatial_hat (bayestme.data.SpatialDifferentialExpressionResult property) spatial_regularizer() (bayestme.svi.deconvolution.BayesTME_VI method) SpatialDifferentialExpressionResult (class in bayestme.data) SpatialExpressionDataset (class in bayestme.data) SPOTS (bayestme.gene_filtering.FilterType attribute) stable_softmax() (in module bayestme.utils)

T

tissue_mask (bayestme.data.SpatialExpressionDataset property)