Classifying Methods within the Framework
To contextualize the above framework, we conducted a limited survey of algorithms and software tools which use networks as prior information in the analysis of omics data and categorized these methods based on the level of network they employ and the computational task(s) they accomplish. Given that hundreds of new algorithms and approaches are published every year, an exhaustive survey is not feasible for the present review. Methods are extremely diverse in their input, operations, and output, but in any case, the overarching goal of these approaches is to produce something that can be perceived and/or interpreted by a human user. We do not include cross-method comparison of features and performance. For each method we give a brief synopsis, discuss key aspects of the method, and finally summarize any real-world applications or validation in a biological system that the authors describe in their manuscript.