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In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics\/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package \u2018transomics2cytoscape\u2019 for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update\/redrawing of trans-omics networks in line with the progress in multi-omics\/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ecell\/transomics2cytoscape\">https:\/\/github.com\/ecell\/transomics2cytoscape<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1038\/s41540-024-00342-8","type":"journal-article","created":{"date-parts":[[2024,2,19]],"date-time":"2024-02-19T06:04:17Z","timestamp":1708322657000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8501-7319","authenticated-orcid":false,"given":"Kozo","family":"Nishida","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junichi","family":"Maruyama","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1982-538X","authenticated-orcid":false,"given":"Kazunari","family":"Kaizu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koichi","family":"Takahashi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2046-4289","authenticated-orcid":false,"given":"Katsuyuki","family":"Yugi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,2,19]]},"reference":[{"key":"342_CR1","doi-asserted-by":"publisher","first-page":"S56","DOI":"10.1038\/nmeth.1436","volume":"7","author":"N Gehlenborg","year":"2010","unstructured":"Gehlenborg, N. et al. 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