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act_ont Cohort
#add_gen_feat Cohort
#add_parentals_of_not_found_hpos_in_regions Top Level Namespace
#add_record Top Level Namespace
#add_record Cohort
add_reference Genomic_Feature
array2genomic_feature Genomic_Feature
#binom Top Level Namespace
#calculate_coverage Top Level Namespace
#calculate_hpo_recovery_and_filter Top Level Namespace
#check Cohort
check_variants Cohort_Parser
#compare_profiles Cohort
#compute_IC_values Top Level Namespace
#compute_hyper_prob Top Level Namespace
#compute_pathway_enrichment Top Level Namespace
#compute_term_list_and_childs Cohort
#compute_windows Genomic_Feature
#coor_overlap? Top Level Namespace
create_cohort Cohort_Parser
#delete Cohort
#download Top Level Namespace
#dummy_cluster_patients Top Level Namespace
#each Genomic_Feature
#each_chr Genomic_Feature
#each_profile Cohort
#each_var Cohort
#export_phenopackets Cohort
#filter_by_term_number Cohort
#generate_cluster_regions Genomic_Feature
#generate_cluster_regions Cohort
#generate_gene_locations Top Level Namespace
#generate_genes_dictionary Top Level Namespace
#generate_hpo_region_matrix Top Level Namespace
#get_and_parse_external_data Top Level Namespace
#get_chr Genomic_Feature
#get_chr_regs Genomic_Feature
#get_cluster_metadata Top Level Namespace
#get_dataset_specifity_index Cohort
#get_detailed_similarity Top Level Namespace
#get_features Genomic_Feature
get_field_numbers2extract Cohort_Parser
get_fields2extract Cohort_Parser
#get_final_coverage Top Level Namespace
#get_general_profile Cohort
#get_genes_by_coordinates Top Level Namespace
#get_ic_analysis Cohort
#get_mean_size Top Level Namespace
get_ontology Cohort
#get_profile Cohort
#get_profile_ic Top Level Namespace
#get_profile_length_at_percentile Cohort
#get_profile_ontology_distribution_tables Cohort
#get_profile_redundancy Cohort
#get_profiles_mean_size Cohort
#get_profiles_terms_frequency Cohort
#get_reference_overlaps Genomic_Feature
#get_region_with_parental_hpo Top Level Namespace
#get_semantic_similarity_clustering Top Level Namespace
#get_similarity_matrix Top Level Namespace
#get_sizes Genomic_Feature
#get_sor_length_distribution Top Level Namespace
#get_summary_sizes Genomic_Feature
#get_summary_stats Top Level Namespace
#get_top_dummy_clusters_stats Top Level Namespace
#get_vars Cohort
#get_vars_sizes Cohort
#group_by_region Top Level Namespace
hash2genomic_feature Genomic_Feature
#hpo_quality_control Top Level Namespace
#index_vars Cohort
#initialize Cohort
#initialize Genomic_Feature
#invert_nested_hash Top Level Namespace
#join_regions Top Level Namespace
#length Genomic_Feature
#link2ont Cohort
load Cohort_Parser
load Reference_parser
#loadBiosistemsInfo Top Level Namespace
#loadFile Top Level Namespace
#load_annotations Genomic_Feature
#load_biosystem2gene_dictionary Top Level Namespace
#load_clustered_patients Top Level Namespace
#load_coordinates Top Level Namespace
#load_evidence_profiles Top Level Namespace
#load_evidences Top Level Namespace
#load_features Genomic_Feature
#load_gene_data Top Level Namespace
#load_hpo_ci_values Top Level Namespace
#load_hpo_ontology Top Level Namespace
load_ontology Cohort
#load_profiles Top Level Namespace
#load_tabular_vars Top Level Namespace
#load_training_file4HPO Top Level Namespace
#load_training_file4regions Top Level Namespace
#load_variants Top Level Namespace
#load_vcf Top Level Namespace
#match Genomic_Feature
#merge Genomic_Feature
#merge_genes_with_kegg_data Top Level Namespace
#parse_clusters_file Top Level Namespace
parse_gtf Reference_parser
#parse_kegg_data Top Level Namespace
#parse_kegg_from_biosystems Top Level Namespace
#parse_patient_results Top Level Namespace
#predict_patient Top Level Namespace
#process_cluster Top Level Namespace
#process_dummy_clustered_patients Top Level Namespace
#profiles Cohort
#read_compressed_json Top Level Namespace
#read_excluded_hpo_file Top Level Namespace
read_excluded_ont_file Cohort
read_records Cohort_Parser
#region_by_to Genomic_Feature
#remove_incomplete_records Cohort
#remove_nested_entries Top Level Namespace
#report_data Top Level Namespace
#save Cohort
#save_patient_matrix Top Level Namespace
#scoring_regions Top Level Namespace
#search4HPO Top Level Namespace
#select_by_profile! Cohort
#select_by_var! Cohort
#system_call Top Level Namespace
#translate_codes Top Level Namespace
#translate_hpos_in_results Top Level Namespace
#write_array Top Level Namespace
#write_arrays4scatterplot Top Level Namespace
#write_cluster_chromosome_data Top Level Namespace
#write_cluster_ic_data Top Level Namespace
#write_compressed_plain_file Top Level Namespace
#write_coverage_data Top Level Namespace
#write_detailed_hpo_profile_evaluation Top Level Namespace
#write_hash Top Level Namespace
#write_matrix_for_R Top Level Namespace
#write_patient_hpo_stat Top Level Namespace
#write_profile_pairs Top Level Namespace
#write_similarity_matrix Top Level Namespace