Roadmap of analysis methods for sex differences in complex diseases. This flowchart outlines a comprehensive approach to analyzing sex differences, progressing from basic data preprocessing to advanced network analysis. Each main category (in colored boxes) represents a distinct class of analytical tools, with sub-categories and specific methods listed below. The hierarchy from top to bottom reflects increasing incorporation of prior biological knowledge and indicates increasing algorithmic complexity. Not every methodology may be required for each application, and the text at the bottom of the boxes indicates when to use each approach. Steps can be iterative and may not always follow a linear progression. While the focus is on interpreting sex differences, these methods are applicable to investigate both sex-dependent and sex-neutral disease-associated changes.