hCoCena: A toolbox for network-based co-expression analysis and horizontal integration of transcriptomic datasets
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Published on: July 29, 2022
Lisa Holsten1, Kilian Dahm2, Marie Oestreich3
1Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE, and University of Bonn, 53127 Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Department of Pediatrics, University Hospital Würzburg, 97080 Würzburg, Germany.
Abstract:
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.
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