Welcome to CompaCt’s documentation!
CompaCt performs automated integrative comparative analysis of large-scale (protein) interaction datasets, identifying groups of interactors (e.g., protein complexes) in parallel in multiple species, allowing systematic identification and comparison of conserved as well as taxon-specific components of protein complexes and other interactions.
Package modules
main: high-level workflow of this project, to run the major steps of the CompaCt analsysis
pairwise_scoring: perform pairwise rbo scoring between interaction datasets
reciprocal_hits: find protein pairs that are reciprocal “top” hits after rbo scoring
MCL_clustering: create combined network from rbo scored data, cluster with MCL, and processes cluster results
process_data: general functions for processing,parsing used file formats and data sctructures.
utils: module with generally useful functions used in multiple modules
API Reference
- compact.main
- compact.pairwise_scoring
- compact.reciprocal_hits
- compact.MCL_clustering
- compact.process_data
parse_settings()get_nested_tags()parse_profile()parse_profiles()flatten_nested_dict()parse_mapping()parse_mappings()fetch_mapping()invert_mapping()split_prot_ids()match_ids()split_match_ids()parse_annotation()parse_scores()parse_top_hits()parse_network()write_network()filter_network()parse_MCL_result()annotate_df()rename_duplicates()remove_appendices()rename_duplicates_int_matrix()add_tag_df()add_tag_multiindex()split_clustmember_tables()parse_gmt()
- compact.utils