hCoCena: A toolbox for network-based co-expression analysis and horizontal integration of transcriptomic datasets

As the number and complexity of transcriptomic datasets increase, there is a rising demand for accessible and user-friendly analysis tools. Here, we present hCoCena (horizontal construction of co-expression networks and analysis), a toolbox facilitating the analysis of a single dataset, as well as the joint analysis of multiple datasets. We describe steps for workspace setup, formatting tables, data processing, and network integration. We then detail procedures for gene clustering, gene set enrichment analysis, and transcription factor enrichment analysis. For complete details on the use and execution of this protocol, please refer to Oestreich et al.1