Index

A

alignment_score() (in module nico_covariations.Covariations), [1]

C

column_group_sub() (in module nico_covariations.utils.pyliger_utilities) compute_PC_space() (in module nico_covariations.Covariations), [1] create_directory() (in module nico_annotations.Annotations), [1] (in module nico_covariations.Covariations), [1] (in module nico_interactions.Interactions), [1]

create_spatial_CT_feature_matrix() (in module nico_interactions.Interactions), [1] create_subtitle() (in module nico_covariations.Covariations), [1]

D

delete_files() (in module nico_annotations.Annotations), [1]

E

euclidean_dist() (in module nico_interactions.Interactions), [1]

extract_and_plot_top_genes_from_chosen_factor_in_celltype() (in module nico_covariations.Covariations), [1]

F

find_all_the_spatial_cells_mapped_to_single_cells() (in module nico_annotations.Annotations), [1] find_anchor_cells_between_ref_and_query() (in module nico_annotations.Annotations), [1] find_annotation_index() (in module nico_annotations.Annotations), [1] find_commnon_MNN() (in module nico_annotations.Annotations), [1] find_correlation_bw_genes_and_PC_component_in_singlecell() (in module nico_covariations.Covariations), [1] find_correlation_bw_genes_and_PC_component_in_singlecell_cosine() (in module nico_covariations.Covariations), [1] find_fold_change() (in module nico_covariations.Covariations), [1] find_index() (in module nico_annotations.Annotations), [1] (in module nico_covariations.Covariations), [1] find_interacting_cell_types() (in module nico_interactions.Interactions), [1]

find_interest_of_genes() (in module nico_covariations.Covariations), [1] find_logistic_regression_interacting_score() (in module nico_covariations.Covariations), [1] find_LR_interactions_in_interacting_cell_types() (in module nico_covariations.Covariations), [1] find_match_index_in_dist() (in module nico_annotations.Annotations), [1] find_mutual_nn() (in module nico_annotations.Annotations), [1] find_neighbors() (in module nico_interactions.Interactions), [1] find_PC_of_invidualCluster_in_SC() (in module nico_covariations.Covariations), [1] find_unmapped_cells_and_deg() (in module nico_annotations.Annotations), [1] findNeighbors_in_given_radius() (in module nico_interactions.Interactions), [1] findSpatialCells() (in module nico_annotations.Annotations), [1] findXYZC() (in module nico_covariations.Covariations), [1]

G

gene_covariation_analysis() (in module nico_covariations.Covariations), [1]

gmean() (in module nico_annotations.utils.SCTransform) (in module utils.SCTransform)

I

iNMF() (in module nico_covariations.utils.pyliger_utilities)

is_outlier() (in module nico_annotations.utils.SCTransform) (in module utils.SCTransform)

M

make_excel_sheet_for_gene_correlation() (in module nico_covariations.Covariations), [1] makePCneighboorhoodFeatureMatrix() (in module nico_covariations.Covariations), [1] model_linear_regression() (in module nico_covariations.Covariations), [1] model_log_regression() (in module nico_interactions.Interactions), [1] module nico_annotations nico_annotations.Annotations, [1] nico_annotations.utils nico_annotations.utils.SCTransform nico_covariations nico_covariations.Covariations, [1] nico_covariations.utils nico_covariations.utils.pyliger_utilities nico_interactions nico_interactions.Interactions, [1] utils utils.SCTransform

multiplicative_method() (in module nico_covariations.Covariations), [1]

N

nico_annotations module nico_annotations.Annotations module, [1] nico_annotations.utils module nico_annotations.utils.SCTransform module nico_based_annotation() (in module nico_annotations.Annotations), [1] nico_covariations module nico_covariations.Covariations module, [1]

nico_covariations.utils module nico_covariations.utils.pyliger_utilities module nico_interactions module nico_interactions.Interactions module, [1] NMF_obj_eval() (in module nico_covariations.utils.pyliger_utilities) nnlsm_blockpivot() (in module nico_covariations.utils.pyliger_utilities) nonneg() (in module nico_covariations.utils.pyliger_utilities) normal_eq_comb() (in module nico_covariations.utils.pyliger_utilities)

P

pathway_analysis() (in module nico_covariations.Covariations), [1] plot_all_ct() (in module nico_annotations.Annotations), [1] (in module nico_covariations.Covariations), [1] plot_coefficient_matrix() (in module nico_interactions.Interactions), [1] plot_confusion_matrix() (in module nico_interactions.Interactions), [1] plot_cosine_and_spearman_correlation_to_factors() (in module nico_covariations.Covariations), [1] plot_evaluation_scores() (in module nico_interactions.Interactions), [1] plot_feature_matrices() (in module nico_covariations.Covariations), [1] plot_ligand_receptor_in_interacting_celltypes() (in module nico_covariations.Covariations), [1]

plot_multiclass_roc() (in module nico_interactions.Interactions), [1] plot_niche_interactions_with_edge_weight() (in module nico_interactions.Interactions), [1] plot_niche_interactions_without_edge_weight() (in module nico_interactions.Interactions), [1] plot_predicted_probabilities() (in module nico_interactions.Interactions), [1] plot_roc_results() (in module nico_interactions.Interactions), [1] plot_significant_regression_covariations_as_circleplot() (in module nico_covariations.Covariations), [1] plot_significant_regression_covariations_as_heatmap() (in module nico_covariations.Covariations), [1] plot_specific_ct() (in module nico_annotations.Annotations), [1] plot_top_genes_for_a_given_celltype_from_all_factors() (in module nico_covariations.Covariations), [1] plot_top_genes_for_pair_of_celltypes_from_two_chosen_factors() (in module nico_covariations.Covariations), [1]

R

read_dist_and_nodes_as_graph() (in module nico_annotations.Annotations), [1] read_LigRecDb() (in module nico_covariations.Covariations), [1] read_processed_data() (in module nico_interactions.Interactions), [1] read_spatial_data() (in module nico_covariations.Covariations), [1] reading_data() (in module nico_interactions.Interactions), [1] remove_extra_character_from_name() (in module nico_annotations.Annotations), [1] (in module nico_covariations.Covariations), [1] (in module nico_interactions.Interactions), [1]

resolved_confused_and_unmapped_mapping_of_cells_with_majority_vote() (in module nico_annotations.Annotations), [1] resolved_confused_and_unmapped_mapping_of_cells_with_weighted_average_of_inverse_distance_in_neighbors() (in module nico_annotations.Annotations), [1] return_singlecells() (in module nico_annotations.Annotations), [1] robust_scale_binned() (in module nico_annotations.utils.SCTransform) (in module utils.SCTransform) run_ridge_regression() (in module nico_covariations.Covariations), [1]

S

save_annotations_in_spatial_object() (in module nico_annotations.Annotations), [1] save_LR_interactions_in_excelsheet_and_regression_summary_in_textfile_for_interacting_cell_types() (in module nico_covariations.Covariations), [1] sct_return_sc_sp_in_shared_common_PC_space() (in module nico_annotations.Annotations), [1] SCTransform() (in module nico_annotations.utils.SCTransform) (in module utils.SCTransform)

sort_index_in_right_order() (in module nico_covariations.Covariations), [1] sorting_of_factors_for_showing_the_value_in_excelsheet() (in module nico_covariations.Covariations), [1] spatial_neighborhood_analysis() (in module nico_interactions.Interactions), [1]

T

theta_ml() (in module nico_annotations.utils.SCTransform) (in module utils.SCTransform)

top_genes_in_correlation_list_without() (in module nico_covariations.Covariations), [1] triangulation_for_triheatmap() (in module nico_covariations.Covariations), [1]

U

utils module

utils.SCTransform module

V

visualize_factors_in_scRNAseq_umap() (in module nico_covariations.Covariations), [1] visualize_factors_in_spatial_umap() (in module nico_covariations.Covariations), [1]

visualize_spatial_anchored_cell_mapped_to_scRNAseq() (in module nico_annotations.Annotations), [1] visualize_umap_and_cell_coordinates_with_all_celltypes() (in module nico_annotations.Annotations), [1] visualize_umap_and_cell_coordinates_with_selected_celltypes() (in module nico_annotations.Annotations), [1]

W

write_annotation() (in module nico_annotations.Annotations), [1]