transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).
Package details |
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Author | Kozo Nishida [aut, cre] (<https://orcid.org/0000-0001-8501-7319>), Katsuyuki Yugi [aut] (<https://orcid.org/0000-0002-2046-4289>) |
Bioconductor views | DataImport KEGG Network Pathways Software |
Maintainer | Kozo Nishida <kozo.nishida@gmail.com> |
License | Artistic-2.0 |
Version | 1.0.0 |
Package repository | View on Bioconductor |
Installation |
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