Index

A

adata_group() (in module sciv.pp) adata_map_df() (in module sciv.pp) add_bernoulli_fluctuation_noise() (in module sciv.tl)

add_noise_perturb() (in module sciv.tl) ami() (in module sciv.tl) ari() (in module sciv.tl) association_score() (in module sciv.ml)

B

bar() (in module sciv.pl) bar_significance() (in module sciv.pl) bar_trait() (in module sciv.pl) barcode_base() (in module sciv.pl) barcode_trait() (in module sciv.pl) barcodes_add_anno() (in module sciv.fl)

base_line() (in module sciv.pl) base_pie() (in module sciv.pl) base_radar() (in module sciv.pl) binary_indicator() (in module sciv.tl) box_base() (in module sciv.pl) box_trait() (in module sciv.pl) bubble() (in module sciv.pl)

C

calculate_fragment_weighted_accessibility() (in module sciv.tl) calculate_init_score_weight() (in module sciv.tl) calinski_harabasz() (in module sciv.tl) check_adata_get() (in module sciv.ul)

check_gpu_availability() (in module sciv.ul) class_bar() (in module sciv.pl) coefficient_of_variation() (in module sciv.tl) communities_graph() (in module sciv.pl) core() (in module sciv.ml)

D

davies_bouldin() (in module sciv.tl) down_sampling_data() (in module sciv.tl) download_sc_atac_file() (in module sciv.dl)

download_trait_file() (in module sciv.dl) download_trs_file() (in module sciv.dl) download_trs_score_file() (in module sciv.dl)

E

euclidean_distances() (in module sciv.tl)

F

file_method() (in module sciv.ul)

filter_data() (in module sciv.pp)

G

gather() (sciv.tl.TraitDataParallel method) generate_hex_colors() (in module sciv.ul) generate_str() (in module sciv.ul) get_difference_genes() (in module sciv.pp) get_difference_peaks() (in module sciv.pp) get_gene_enrichment() (in module sciv.pp) get_gene_expression() (in module sciv.pp)

get_index() (in module sciv.ul) get_peak_matrix() (in module sciv.pp) get_real_predict_label() (in module sciv.ul) get_sc_atac() (in module sciv.pp) get_tf_data() (in module sciv.pp) graph() (in module sciv.pl) gsea_enrichr() (in module sciv.pp)

H

heatmap() (in module sciv.pl)

heatmap_annotation() (in module sciv.pl)

I

is_asc_sort() (in module sciv.tl)

J

jaccard_similarity() (in module sciv.tl)

K

k_means() (in module sciv.tl) kde() (in module sciv.pl)

kl_divergence() (in module sciv.tl) knock() (in module sciv.ml)

L

list_duplicate_set() (in module sciv.ul) list_index() (in module sciv.ul)

log() (in module sciv.ul) lsi() (in module sciv.tl)

M

manhattan_causal_variant() (in module sciv.pl) marginal_normalize() (in module sciv.tl) matrix_callback_block_storage() (in module sciv.tl) matrix_division_block_storage() (in module sciv.tl) matrix_dot_block_storage() (in module sciv.tl) matrix_multiply_block_storage() (in module sciv.tl) matrix_operation_memory_efficient() (in module sciv.tl) mean_symmetric_scale() (in module sciv.tl) merge_matrix() (in module sciv.tl) (in module sciv.ul)

merge_sc_atac() (in module sciv.pp) min_max_norm() (in module sciv.tl) module sciv.dl sciv.fl sciv.ml sciv.pl, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] sciv.pp sciv.tl, [1], [2] sciv.ul

N

network_two_types() (in module sciv.pl)

numerical_bisection_step() (in module sciv.ul)

O

obtain_cell_cell_network() (in module sciv.tl)

overlap() (in module sciv.tl) overlap_sum() (in module sciv.tl)

P

paga_trajectory() (in module sciv.pp) pca() (in module sciv.tl) perturb_data() (in module sciv.tl)

pie_label() (in module sciv.pl) pie_trait() (in module sciv.pl) poisson_vi() (in module sciv.pp) pseudo_time_score() (in module sciv.pl)

R

radar() (in module sciv.pl) radar_trait() (in module sciv.pl) random_walk() (in module sciv.tl) RandomWalk (class in sciv.tl) rate_bar_plot() (in module sciv.pl) rate_circular_bar_plot() (in module sciv.pl) read_barcodes_file() (in module sciv.fl) read_h5() (in module sciv.fl) read_h5ad() (in module sciv.fl) read_pkl() (in module sciv.fl) read_sc_atac() (in module sciv.fl) read_sc_atac_10x_h5() (in module sciv.fl) read_sc_atac_file() (in module sciv.dl) read_trait_file() (in module sciv.dl)

read_trs_file() (in module sciv.dl) read_trs_score_file() (in module sciv.dl) read_variants() (in module sciv.fl) run_ablation_m_knn() (sciv.tl.RandomWalk method) run_ablation_ncsw() (sciv.tl.RandomWalk method) run_ablation_ncw() (sciv.tl.RandomWalk method) run_ablation_nsw() (sciv.tl.RandomWalk method) run_benchmark() (sciv.tl.RandomWalk method) run_core() (sciv.tl.RandomWalk method) run_en_ablation_m_knn() (sciv.tl.RandomWalk method) run_en_ablation_ncsw() (sciv.tl.RandomWalk method) run_en_ablation_ncw() (sciv.tl.RandomWalk method) run_en_ablation_nsw() (sciv.tl.RandomWalk method) run_enrichment() (sciv.tl.RandomWalk method) run_knock() (sciv.tl.RandomWalk method)

S

safe_kl_divergence() (in module sciv.tl) save_h5() (in module sciv.fl) save_h5ad() (in module sciv.fl) save_pkl() (in module sciv.fl) scale_norm() (sciv.tl.RandomWalk static method) scatter() (sciv.tl.TraitDataParallel method) scatter_3d() (in module sciv.pl) scatter_atac() (in module sciv.pl) scatter_base() (in module sciv.pl) scatter_trait() (in module sciv.pl) sciv.dl module sciv.fl module sciv.ml module sciv.pl module, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]

sciv.pp module sciv.tl module, [1], [2] sciv.ul module semi_mutual_knn_weight() (in module sciv.tl) set_inf_value() (in module sciv.ul) sigmoid() (in module sciv.tl) silhouette() (in module sciv.tl) spectral_clustering() (in module sciv.tl) spectral_eigenmaps() (in module sciv.tl) split_matrix() (in module sciv.tl) (in module sciv.ul) strings_map_numbers() (in module sciv.ul) sum_min_max() (in module sciv.ul) symmetric_scale() (in module sciv.tl)

T

tf_idf() (in module sciv.tl) three_venn() (in module sciv.pl) to_dense() (in module sciv.ul) to_fragments() (in module sciv.fl) to_meta() (in module sciv.fl) to_sparse() (in module sciv.ul)

track_with_memory() (in module sciv.ul) TraitDataParallel (class in sciv.tl) trs_scale_norm() (in module sciv.tl) tsne() (in module sciv.tl) two_bar() (in module sciv.pl) two_venn() (in module sciv.pl)

U

umap() (in module sciv.tl)

V

vector_multiply_block_storage() (in module sciv.tl) violin_base() (in module sciv.pl)

violin_trait() (in module sciv.pl) volcano_base() (in module sciv.pl)

Z

z_score_marginal() (in module sciv.tl)

z_score_normalize() (in module sciv.tl) z_score_to_p_value() (in module sciv.tl)