Metabolic Pathway Completeness and Abundance Calculation
Add Missing Rows to a Data Frame
Calculate Log2 Ratio of Sample Values to Row Means
Convert Abundance Values to Presence/Absence Indicators
Create and Export Pathway-Specific Module Sample Files
Escape Special Characters in a String
Extract Innermost Parentheses Content
Group KO Abundance Data by Module
Metabolic Pathway Coverage Analysis
Merge Module Information with Module Table
Process All Modules in Pathway Information
Process All Pathways Analysis
Process Module Brackets Recursively
Process Module Definition String
Process Module Components with Comma Handling
Process Module Components with Plus and Comma Handling
Process Module Components with Plus Sign Handling
Process Module Steps with Complex KO String Handling
Process Module Structure Data
Process Comma-Separated KOs with Specified Scaling Method
Direct KO Processing Without Special Handling
Process Plus-Separated KOs with Specified Scaling Method
Process Space-Separated KOs with Mean Calculation
Read and Process KO Sample Table with Pathway Information
Read and process Pathway information dataframe
Remove Outer Parentheses from String
Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies. Supports both completeness (presence/absence) and abundance-weighted analyses. Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.