Index

A

adata_to_mtx() (in module sctriangulate.preprocessing) add_annotations() (in module sctriangulate.preprocessing) add_azimuth() (in module sctriangulate.preprocessing)

add_new_metrics() (in module sctriangulate.main_class.ScTriangulate) add_to_invalid() (in module sctriangulate.main_class.ScTriangulate) add_to_invalid_by_win_fraction() (in module sctriangulate.main_class.ScTriangulate) add_umap() (in module sctriangulate.preprocessing)

B

bg_greyed_cmap() (in module sctriangulate.colors)

build_custom_continuous_cmap() (in module sctriangulate.colors) build_custom_divergent_cmap() (in module sctriangulate.colors)

C

clear_invalid() (in module sctriangulate.main_class.ScTriangulate) CLR_normalization() (sctriangulate.preprocessing.Normalization static method) cluster_level_spatial_stability() (in module sctriangulate.spatial) cluster_performance() (in module sctriangulate.main_class.ScTriangulate) color_stdout() (in module sctriangulate.colors)

colors_for_set() (in module sctriangulate.colors) compute_metrics() (in module sctriangulate.main_class.ScTriangulate) compute_shapley() (in module sctriangulate.main_class.ScTriangulate) concat_rna_and_other() (in module sctriangulate.preprocessing) confusion_to_df() (in module sctriangulate.main_class.ScTriangulate) create_spatial_features() (in module sctriangulate.spatial)

D

deserialize() (in module sctriangulate.main_class.ScTriangulate) display_hierarchy() (in module sctriangulate.main_class.ScTriangulate)

doublet_predict() (in module sctriangulate.main_class.ScTriangulate) (in module sctriangulate.preprocessing)

E

elo_rating_like() (in module sctriangulate.main_class.ScTriangulate)

ensemblgene_to_symbol() (sctriangulate.preprocessing.GeneConvert static method) extract_stability() (in module sctriangulate.main_class.ScTriangulate)

F

find_genes() (in module sctriangulate.preprocessing)

format_find_concat() (in module sctriangulate.preprocessing)

G

gene_activity_count_matrix_new_10x() (in module sctriangulate.preprocessing) gene_activity_count_matrix_old_10x() (in module sctriangulate.preprocessing) gene_to_df() (in module sctriangulate.main_class.ScTriangulate) GeneConvert (class in sctriangulate.preprocessing)

generate_block() (in module sctriangulate.colors) generate_gradient() (in module sctriangulate.colors) get_metrics_and_shapley() (in module sctriangulate.main_class.ScTriangulate) GMM_normalization() (sctriangulate.preprocessing.Normalization static method) gradienting() (in module sctriangulate.colors)

I

identify_ecosystem() (in module sctriangulate.spatial)

identify_spatial_program() (in module sctriangulate.spatial)

J

just_log_norm() (in module sctriangulate.preprocessing)

L

large_txt_to_mtx() (in module sctriangulate.preprocessing)

lazy_run() (in module sctriangulate.main_class.ScTriangulate)

M

make_sure_adata_writable() (in module sctriangulate.preprocessing) make_sure_mat_dense() (in module sctriangulate.preprocessing) make_sure_mat_sparse() (in module sctriangulate.preprocessing)

modality_contributions() (in module sctriangulate.main_class.ScTriangulate) mtx_to_adata() (in module sctriangulate.preprocessing) mtx_to_large_txt() (in module sctriangulate.preprocessing)

N

nca_embedding() (in module sctriangulate.preprocessing)

Normalization (class in sctriangulate.preprocessing)

P

penalize_artifact() (in module sctriangulate.main_class.ScTriangulate) pick_n_colors() (in module sctriangulate.colors) plot_cluster_feature() (in module sctriangulate.main_class.ScTriangulate) plot_clusterability() (in module sctriangulate.main_class.ScTriangulate) plot_concordance() (in module sctriangulate.main_class.ScTriangulate) plot_confusion() (in module sctriangulate.main_class.ScTriangulate) plot_deconvolution() (in module sctriangulate.spatial)

plot_heterogeneity() (in module sctriangulate.main_class.ScTriangulate) plot_long_heatmap() (in module sctriangulate.main_class.ScTriangulate) plot_multi_modal_feature_rank() (in module sctriangulate.main_class.ScTriangulate) plot_stability() (in module sctriangulate.main_class.ScTriangulate) plot_two_column_sankey() (in module sctriangulate.main_class.ScTriangulate) plot_umap() (in module sctriangulate.main_class.ScTriangulate) plot_winners_statistics() (in module sctriangulate.main_class.ScTriangulate) pruning() (in module sctriangulate.main_class.ScTriangulate)

R

read_spatial_data() (in module sctriangulate.spatial) reformat_peak() (in module sctriangulate.preprocessing) regress_out_size_effect() (in module sctriangulate.main_class.ScTriangulate)

retrieve_pretty_cmap() (in module sctriangulate.colors) retrieve_pretty_colors() (in module sctriangulate.colors) rna_umap_transform() (in module sctriangulate.preprocessing) run_single_key_assessment() (in module sctriangulate.main_class.ScTriangulate)

S

salvage_run() (in module sctriangulate.main_class.ScTriangulate) scanpy_recipe() (in module sctriangulate.preprocessing)

ScTriangulate (class in sctriangulate.main_class) serialize() (in module sctriangulate.main_class.ScTriangulate) small_txt_to_adata() (in module sctriangulate.preprocessing)

T

total_normalization() (sctriangulate.preprocessing.Normalization static method)

U

umap_color_exceed_102() (in module sctriangulate.preprocessing)

umap_dual_view_save() (in module sctriangulate.preprocessing)

V

viewer_cluster_feature_figure() (in module sctriangulate.main_class.ScTriangulate) viewer_cluster_feature_html() (in module sctriangulate.main_class.ScTriangulate)

viewer_heterogeneity_figure() (in module sctriangulate.main_class.ScTriangulate) viewer_heterogeneity_html() (in module sctriangulate.main_class.ScTriangulate)