Fig. 6

State-of-the-art tools for geneset network analysis. Comparison between publicly available, documented and actively maintained network analysis tools. For each tool, we reviewed the type of networks and genesets that can be given as input (e.g. multi-organism, external/custom defined), and whether a tool can generate tables and figures. The majority of tools provides only one type of network analysis, either GNT or GNA, with few of them providing association tests between multiple user defined genesets. We also noted that, for many tools, there are no statistical testing procedures. Conversely, PyGNA enables comprehensive statistical network analysis under different interaction models, testing both single geneset topology and multiple genesets association. Moreover, PyGNA takes input user-defined networks, regardless of their type and organism, and provides results in comma separated value (CSV) files and PDF figures