Index

A

affinity() (in module tacco.tools) anndata2dataframe() (in module tacco.utils) AnnData_query() (in module tacco.utils) annotate() (in module tacco.tools) annotate_NMFreg() (in module tacco.tools) annotate_nnls() (in module tacco.tools) annotate_novosparc() (in module tacco.tools) annotate_OT() (in module tacco.tools) annotate_projection() (in module tacco.tools) annotate_RCTD() (in module tacco.tools) annotate_single_molecules() (in module tacco.tools) annotate_SingleR() (in module tacco.tools) annotate_svm() (in module tacco.tools)

annotate_tangram() (in module tacco.tools) annotate_wot() (in module tacco.tools) annotated_heatmap() (in module tacco.plots) annotation_coordinate() (in module tacco.plots) (in module tacco.tools) apply_random_platform_effect() (in module tacco.preprocessing) assert_adata_equal() (in module tacco.testing) assert_dense_equal() (in module tacco.testing) assert_frame_equal() (in module tacco.testing) assert_index_equal() (in module tacco.testing) assert_series_equal() (in module tacco.testing) assert_sparse_equal() (in module tacco.testing) assert_tuple_equal() (in module tacco.testing)

B

benchmark_annotate() (in module tacco.benchmarking) benchmark_script() (in module tacco.benchmarking)

benchmark_shell() (in module tacco.benchmarking) bin() (in module tacco.utils)

C

cdist() (in module tacco.utils) cellsize() (in module tacco.plots) check_counts_validity() (in module tacco.preprocessing) co_occurrence() (in module tacco.plots) (in module tacco.tools) co_occurrence_matrix() (in module tacco.plots) (in module tacco.tools) col_scale() (in module tacco.utils)

comparison() (in module tacco.plots) complete_choice() (in module tacco.utils) compositions() (in module tacco.plots) construct_reference_profiles() (in module tacco.preprocessing) contribution() (in module tacco.plots) coo_tocsr_buffered() (in module tacco.utils) coo_tocsr_inplace() (in module tacco.utils) counts() (in module tacco.get) cpu_count() (in module tacco.utils)

D

data_from_key() (in module tacco.get) dataframe2anndata() (in module tacco.utils) dense_distance_matrix() (in module tacco.utils)

distance_matrix() (in module tacco.tools) distribute_molecules() (in module tacco.tools) divide() (in module tacco.utils) dotplot() (in module tacco.plots)

E

enrichments() (in module tacco.tools)

F

fill_regions() (in module tacco.tools) filter() (in module tacco.preprocessing) filter_annotation() (in module tacco.preprocessing) filter_profiles() (in module tacco.preprocessing) filter_reference() (in module tacco.preprocessing) filter_reference_genes() (in module tacco.preprocessing)

find_regions() (in module tacco.tools) find_unused_key() (in module tacco.utils) fishers_exact() (in module tacco.utils) flat_inverse_mapping() (in module tacco.utils) frequency() (in module tacco.plots) frequency_bar() (in module tacco.plots)

G

gemmT() (in module tacco.utils) generate_mixture_profiles() (in module tacco.utils) get_average_profiles() (in module tacco.utils) get_balanced_separated_intervals() (in module tacco.utils) get_compositions() (in module tacco.tools)

get_contributions() (in module tacco.tools) get_default_colors() (in module tacco.plots) get_first_principal_axis() (in module tacco.utils) get_maximum_annotation() (in module tacco.utils) get_sum() (in module tacco.utils)

H

hash() (in module tacco.utils)

heapsort3() (in module tacco.utils) heatmap() (in module tacco.plots)

L

log() (in module tacco.utils)

log1p() (in module tacco.utils)

M

mannwhitneyu() (in module tacco.utils) merge_annotation() (in module tacco.utils) merge_colors() (in module tacco.utils) merge_observations() (in module tacco.tools) min_dtype() (in module tacco.utils) mix_base_colors() (in module tacco.plots) mix_in_silico() (in module tacco.tools) mode() (in module tacco.utils)

module tacco tacco.benchmarking tacco.get tacco.plots tacco.preprocessing tacco.testing tacco.tools tacco.utils

N

normalize_platform() (in module tacco.preprocessing)

P

parallel_nnls() (in module tacco.utils) positions() (in module tacco.get)

preprocess_single_cell_data() (in module tacco.utils) projection() (in module tacco.utils)

R

refine_reference() (in module tacco.preprocessing) row_scale() (in module tacco.utils)

run_goa_analysis() (in module tacco.tools) run_orthology_converter() (in module tacco.tools)

S

scale_counts() (in module tacco.utils) scatter() (in module tacco.plots) segment() (in module tacco.tools) setup_goa_analysis() (in module tacco.tools) setup_orthology_converter() (in module tacco.tools) sigmap() (in module tacco.plots) significances() (in module tacco.plots) solve_OT() (in module tacco.utils) sparse_distance_matrix() (in module tacco.utils) sparse_result_gemmT() (in module tacco.utils)

spatial_split() (in module tacco.utils) spectral_clustering() (in module tacco.tools) split_observations() (in module tacco.tools) split_spatial_samples() (in module tacco.utils) sqrt() (in module tacco.utils) string_decode() (in module tacco.testing) string_encode() (in module tacco.testing) studentttest() (in module tacco.utils) subplots() (in module tacco.plots) subsample_annotation() (in module tacco.preprocessing) sum() (in module tacco)

T

tacco module tacco.benchmarking module tacco.get module tacco.plots module

tacco.preprocessing module tacco.testing module tacco.tools module tacco.utils module tsne_single_cell_data() (in module tacco.utils)

U

umap_single_cell_data() (in module tacco.utils)

W

welchttest() (in module tacco.utils)

write_adata_x_var_obs() (in module tacco.utils)