Complex systems thinking is applied to a wide variety of domains, from neuroscience to computer science and economics. The wide variety of implementations has resulted in two key challenges: the progenation of many domain-specific strategies that are seldom revisited or questioned, and the siloing of ideas within a domain due to inconsistency of complex systems language. In this work we offer basic, domain-agnostic language in order to advance towards a more cohesive vocabulary. We use this language to evaluate each step of the complex systems analysis pipeline, beginning with the system and data collected, then moving through different mathematical formalisms for encoding the observed data (i.e. graphs, simplicial complexes, and hypergraphs), and relevant computational methods for each formalism. At each step we consider different types of \emph{dependencies}; these are properties of the system that describe how the existence of one relation among the parts of a system may influence the existence of another relation. We discuss how dependencies may arise and how they may alter interpretation of results or the entirety of the analysis pipeline. We close with two real-world examples using coauthorship data and email communications data that illustrate how the system under study, the dependencies therein, the research question, and choice of mathematical representation influence the results. We hope this work can serve as an opportunity of reflection for experienced complexity scientists, as well as an introductory resource for new researchers.