Index

A

adata (celloracle.Oracle attribute) addAnnotation() (celloracle.Net method) (celloracle.network.Net method) addTFinfo_dictionary() (celloracle.Net method) (celloracle.network.Net method) (celloracle.Oracle method)

addTFinfo_matrix() (celloracle.Net method) (celloracle.network.Net method) all_genes (celloracle.Net attribute) (celloracle.network.Net attribute) all_target_gene (celloracle.motif_analysis.TFinfo attribute) annotation (celloracle.Net attribute) (celloracle.network.Net attribute)

C

calculate_mass_filter() (celloracle.Oracle method) calculate_p_mass() (celloracle.Oracle method) calculate_randomized_coef_table() (celloracle.Oracle method) celloracle module celloracle.data module celloracle.data_conversion module celloracle.go_analysis module celloracle.motif_analysis module celloracle.network module celloracle.network_analysis module

celloracle.utility module cellstate (celloracle.Net attribute) (celloracle.network.Net attribute) change_cluster_unit() (celloracle.Oracle method) check_peak_format() (in module celloracle.motif_analysis) check_python_requirements() (in module celloracle) clip_delta_X() (celloracle.Oracle method) cluster (celloracle.Links attribute) (celloracle.network_analysis.Links attribute) cluster_column_name (celloracle.Oracle attribute) coefs_dict (celloracle.Net attribute) (celloracle.network.Net attribute) copy() (celloracle.motif_analysis.TFinfo method) (celloracle.Net method) (celloracle.network.Net method) (celloracle.Oracle method) count_cells_in_mc_resutls() (celloracle.Oracle method)

D

dic_peak2Targetgene (celloracle.motif_analysis.TFinfo attribute) dic_targetgene2TFs (celloracle.motif_analysis.TFinfo attribute)

dic_TF2targetgenes (celloracle.motif_analysis.TFinfo attribute) draw_network() (in module celloracle.network_analysis)

E

embedding_name (celloracle.Net attribute) (celloracle.network.Net attribute) (celloracle.Oracle attribute) estimate_impact_of_perturbations_under_various_ns() (celloracle.Oracle method)

evaluate_and_plot_simulation_value_distribution() (celloracle.Oracle method) evaluate_simulated_gene_distribution_range() (celloracle.Oracle method) exec_process() (in module celloracle.utility) extract_active_gene_lists() (celloracle.Oracle method)

F

failed_genes (celloracle.Net attribute) (celloracle.network.Net attribute) filter_links() (celloracle.Links method) (celloracle.network_analysis.Links method) filter_motifs_by_score() (celloracle.motif_analysis.TFinfo method) filter_peaks() (celloracle.motif_analysis.TFinfo method) filtered_links (celloracle.Links attribute) (celloracle.network_analysis.Links attribute)

fit_All_genes() (celloracle.Net method) (celloracle.network.Net method) fit_All_genes_parallel() (celloracle.Net method) (celloracle.network.Net method) fit_genes() (celloracle.Net method) (celloracle.network.Net method) fit_GRN_for_simulation() (celloracle.Oracle method) fitted_genes (celloracle.Net attribute) (celloracle.network.Net attribute)

G

gem (celloracle.Net attribute) (celloracle.network.Net attribute) gem_standerdized (celloracle.Net attribute) (celloracle.network.Net attribute) geneID2Symbol() (in module celloracle.go_analysis) geneSymbol2ID() (in module celloracle.go_analysis) get_cluster_specific_TFdict_from_Links() (celloracle.Oracle method) get_GO() (in module celloracle.go_analysis) get_links() (celloracle.Oracle method) (in module celloracle.network_analysis)

get_markov_simulation_cell_transition_table() (celloracle.Oracle method) get_markvov_simulation_cell_transition_table() (celloracle.Oracle method) get_network_entropy() (celloracle.Links method) (celloracle.network_analysis.Links method) get_network_score() (celloracle.Links method) (celloracle.network_analysis.Links method) get_R_path() (in module celloracle.network_analysis) get_score() (celloracle.Links method) (celloracle.network_analysis.Links method) get_tss_info() (in module celloracle.motif_analysis) getDF_TGxTF() (in module celloracle.network)

I

import_anndata_as_normalized_count() (celloracle.Oracle method) import_anndata_as_raw_count() (celloracle.Oracle method) import_TF_data() (celloracle.Oracle method)

info() (celloracle.utility.makelog method) integrate_tss_peak_with_cicero() (in module celloracle.motif_analysis) intersect() (in module celloracle.utility) is_genome_installed() (in module celloracle.motif_analysis)

K

knn_data_transferer() (in module celloracle.utility)

L

library_last_update_date (celloracle.Net attribute) (celloracle.network.Net attribute) linkList (celloracle.Net attribute) (celloracle.network.Net attribute) linkList_to_networkgraph() (in module celloracle.network_analysis) Links (class in celloracle) (class in celloracle.network_analysis) links_dict (celloracle.Links attribute) (celloracle.network_analysis.Links attribute) load_Celegans_promoter_base_GRN() (in module celloracle.data) load_chicken_promoter_base_GRN() (in module celloracle.data) load_drosophila_promoter_base_GRN() (in module celloracle.data) load_hdf5() (in module celloracle) (in module celloracle.utility) load_human_promoter_base_GRN() (in module celloracle.data)

load_links() (in module celloracle.network_analysis) load_motifs() (in module celloracle.motif_analysis) load_mouse_promoter_base_GRN() (in module celloracle.data) load_net_from_patquets() (in module celloracle.network) load_pickled_object() (in module celloracle.utility) load_Pig_promoter_base_GRN() (in module celloracle.data) load_rat_promoter_base_GRN() (in module celloracle.data) load_Scerevisiae_promoter_base_GRN() (in module celloracle.data) load_TFinfo() (in module celloracle.motif_analysis) load_TFinfo_df_mm9_mouse_atac_atlas() (in module celloracle.data) load_TFinfo_from_parquets() (in module celloracle.motif_analysis) load_tutorial_links_object() (in module celloracle.data) load_tutorial_oracle_object() (in module celloracle.data) load_xenopus_tropicalis_promoter_base_GRN() (in module celloracle.data) load_zebrafish_promoter_base_GRN() (in module celloracle.data)

M

make_TFinfo_dataframe_and_dictionary() (celloracle.motif_analysis.TFinfo method) make_TFinfo_from_scanned_file() (in module celloracle.motif_analysis) makelog (class in celloracle.utility) merged_score (celloracle.Links attribute) (celloracle.network_analysis.Links attribute) module celloracle celloracle.data celloracle.data_conversion celloracle.go_analysis celloracle.motif_analysis celloracle.network celloracle.network_analysis celloracle.utility

N

name (celloracle.Links attribute) (celloracle.network_analysis.Links attribute)

Net (class in celloracle) (class in celloracle.network)

O

object_initiation_date (celloracle.Net attribute) (celloracle.network.Net attribute)

Oracle (class in celloracle)

P

palette (celloracle.Links attribute) (celloracle.network_analysis.Links attribute) peak2fasta() (in module celloracle.motif_analysis) peak_df (celloracle.motif_analysis.TFinfo attribute) plot_cartography_scatter_per_cluster() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_cartography_term() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_degree_distributions() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_mc_results_as_kde() (celloracle.Oracle method) plot_mc_results_as_sankey() (celloracle.Oracle method) plot_mc_results_as_trajectory() (celloracle.Oracle method)

plot_network_entropy_distributions() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_score_comparison_2D() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_score_discributions() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_score_per_cluster() (celloracle.Links method) (celloracle.network_analysis.Links method) plot_scores_as_rank() (celloracle.Links method) (celloracle.network_analysis.Links method) plotCoefs() (celloracle.Net method) (celloracle.network.Net method) prepare_markov_simulation() (celloracle.Oracle method)

R

read_bed() (in module celloracle.motif_analysis) ref_genome (celloracle.motif_analysis.TFinfo attribute) remove_zero_seq() (in module celloracle.motif_analysis)

reset_dictionary_and_df() (celloracle.motif_analysis.TFinfo method) reset_filtering() (celloracle.motif_analysis.TFinfo method) run_markov_chain_simulation() (celloracle.Oracle method)

S

save_as_parquet() (celloracle.motif_analysis.TFinfo method) save_as_pickled_object() (in module celloracle.utility) scan() (celloracle.motif_analysis.TFinfo method) scan_dna_for_motifs() (in module celloracle.motif_analysis) scanned_df (celloracle.motif_analysis.TFinfo attribute) set_motifs() (celloracle.motif_analysis.TFinfo method) set_R_path() (in module celloracle.network_analysis)

seurat_object_to_anndata() (in module celloracle.data_conversion) simulate_shift() (celloracle.Oracle method) standard() (in module celloracle.utility) stats_dict (celloracle.Net attribute) (celloracle.network.Net attribute) suggest_mass_thresholds() (celloracle.Oracle method) summarize_mc_results_by_cluster() (celloracle.Oracle method)

T

test_R_libraries_installation() (in module celloracle) TFinfo (celloracle.Net attribute) (celloracle.network.Net attribute) (class in celloracle.motif_analysis) to_dataframe() (celloracle.motif_analysis.TFinfo method) to_dictionary() (celloracle.motif_analysis.TFinfo method) to_hdf5() (celloracle.Links method) (celloracle.motif_analysis.TFinfo method) (celloracle.Net method) (celloracle.network.Net method) (celloracle.network_analysis.Links method) (celloracle.Oracle method)

transfer_all_colors_between_anndata() (in module celloracle.utility) transfer_color_between_anndata() (in module celloracle.utility) transfer_scores_from_links_to_adata() (in module celloracle.network_analysis)

U

update_adata() (in module celloracle.utility) update_cluster_colors() (celloracle.Oracle method) updateLinkList() (celloracle.Net method) (celloracle.network.Net method)

updateTFinfo_dictionary() (celloracle.Net method) (celloracle.network.Net method) (celloracle.Oracle method)