hCoCena: horizontal integration and analysis of transcriptomics datasets

MOTIVATION: Transcriptome-based gene co-expression analysis has become a standard procedure for structured and contextualized understanding and comparison of different conditions and phenotypes. Since large study designs with a broad variety of conditions are costly and laborious, extensive comparisons are hindered when utilizing only a single dataset. Thus, there is an increased need for tools that allow the integration of multiple transcriptomic datasets with subsequent joint analysis, which can provide a more systematic understanding of gene co-expression and co-functionality within and across conditions. To make such an integrative analysis accessible to a wide spectrum of users with differing levels of programming expertise it is essential to provide user-friendliness and customizability as well as thorough documentation. RESULTS: This article introduces horizontal CoCena (hCoCena: horizontal construction of co-expression networks and analysis), an R-package for network-based co-expression analysis that allows the analysis of a single transcriptomic dataset as well as the joint analysis of multiple datasets. With hCoCena, we provide a freely available, user-friendly and adaptable tool for integrative multi-study or single-study transcriptomics analyses alongside extensive comparisons to other existing tools. AVAILABILITY AND IMPLEMENTATION: The hCoCena R-package is provided together with R Markdowns that implement an exemplary analysis workflow including extensive documentation and detailed descriptions of data structures and objects. Such efforts not only make the tool easy to use but also enable the seamless integration of user-written scripts and functions into the workflow, creating a tool that provides a clear design while remaining flexible and highly customizable. The package and additional information including an extensive Wiki are freely available on GitHub: https://github.com/MarieOestreich/hCoCena. The version at the time of writing has been added to Zenodo under the following link: https://doi.org/10.5281/zenodo.6911782. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.