KO_Sample_wide          KEGG Orthology (KO) Abundance/Presence Across
                        Microbial Samples or Genomes
KO_pathway_ref          KEGG Orthology (KO) Pathway Information Dataset
add_rows_if_not_exists
                        Add Missing Rows to a Data Frame
ata_cal                 Calculate Log2 Ratio of Sample Values to Row
                        Means
convert_abundance_to_presence
                        Convert Abundance Values to Presence/Absence
                        Indicators
create_sub_module_sample
                        Create and Export Pathway-Specific Module
                        Sample Files
escape_special_chars    Escape Special Characters in a String
extract_inner_brackets
                        Extract Innermost Parentheses Content
group_ko_by_module      Group KO Abundance Data by Module
mclink                  Metabolic Pathway Coverage Analysis
merge_module_name       Merge Module Information with Module Table
process_all_modules     Process All Modules in Pathway Information
process_all_pathways    Process All Pathways Analysis
process_module_brackets
                        Process Module Brackets Recursively
process_module_definition
                        Process Module Definition String
process_module_loop_comma
                        Process Module Components with Comma Handling
process_module_loop_plu_comma
                        Process Module Components with Plus and Comma
                        Handling
process_module_loop_plus
                        Process Module Components with Plus Sign
                        Handling
process_module_step     Process Module Steps with Complex KO String
                        Handling
process_module_structure
                        Process Module Structure Data
process_step_comma      Process Comma-Separated KOs with Specified
                        Scaling Method
process_step_direct     Direct KO Processing Without Special Handling
process_step_plus       Process Plus-Separated KOs with Specified
                        Scaling Method
process_step_space      Process Space-Separated KOs with Mean
                        Calculation
read_and_process_KO_table
                        Read and Process KO Sample Table with Pathway
                        Information
read_and_process_pathway_infor
                        Read and process Pathway information dataframe
remove_outer_brackets   Remove Outer Parentheses from String
