Index

A

add_tag_df() (in module compact.process_data)

add_tag_multiindex() (in module compact.process_data) annotate_df() (in module compact.process_data)

B

between_scoring() (in module compact.main)

C

compact.main module compact.MCL_clustering module compact.pairwise_scoring module compact.process_data module

compact.reciprocal_hits module compact.utils module correlate_samples() (in module compact.utils) create_combined_network() (in module compact.MCL_clustering)

D

det_search_depth() (in module compact.pairwise_scoring)

determine_top_weightedness() (in module compact.pairwise_scoring) download_sample_abuns() (in module compact.utils)

E

eprint() (in module compact.utils)

F

fetch_mapping() (in module compact.process_data)

filter_network() (in module compact.process_data) flatten_nested_dict() (in module compact.process_data)

G

get_cluster_max_fraction() (in module compact.utils) get_col_mapping() (in module compact.utils) get_comp_mapping() (in module compact.utils) get_comparison_matches() (in module compact.utils)

get_nested_tags() (in module compact.process_data) get_reciprocal_top_hits() (in module compact.reciprocal_hits) get_sample_tags() (in module compact.utils) get_stripped_mapping() (in module compact.utils)

I

invert_mapping() (in module compact.process_data) (in module compact.utils)

M

main() (in module compact.main) map_df_index() (in module compact.utils) match_ids() (in module compact.process_data) mcl_available() (in module compact.utils) mcl_clustering() (in module compact.main) module compact.main compact.MCL_clustering compact.pairwise_scoring compact.process_data compact.reciprocal_hits compact.utils

P

pairwise_rbo_scoring() (in module compact.pairwise_scoring) parse_annotation() (in module compact.process_data) parse_gmt() (in module compact.process_data) parse_mapping() (in module compact.process_data) parse_mappings() (in module compact.process_data) parse_MCL_result() (in module compact.process_data) parse_network() (in module compact.process_data)

parse_profile() (in module compact.process_data) parse_profiles() (in module compact.process_data) parse_scores() (in module compact.process_data) parse_settings() (in module compact.process_data) parse_top_hits() (in module compact.process_data) process_annot_MCL_res() (in module compact.MCL_clustering) process_mcl_result() (in module compact.main)

R

remove_appendices() (in module compact.process_data) rename_duplicates() (in module compact.process_data)

rename_duplicates_int_matrix() (in module compact.process_data) run_MCL() (in module compact.MCL_clustering)

S

save_results() (in module compact.main) score_comparison() (in module compact.main) separate_subclusters() (in module compact.MCL_clustering)

split_clustmember_tables() (in module compact.process_data) split_match_ids() (in module compact.process_data) split_prot_ids() (in module compact.process_data)

W

write_network() (in module compact.process_data)