Package: transomics2cytoscape 1.17.0
Kozo Nishida
transomics2cytoscape: A tool set for 3D Trans-Omic network visualization with Cytoscape
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).
Authors:
transomics2cytoscape_1.17.0.tar.gz
transomics2cytoscape_1.17.0.zip(r-4.5)transomics2cytoscape_1.17.0.zip(r-4.4)transomics2cytoscape_1.17.0.zip(r-4.3)
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transomics2cytoscape.pdf |transomics2cytoscape.html✨
transomics2cytoscape/json (API)
NEWS
| # Install 'transomics2cytoscape' in R: |
| install.packages('transomics2cytoscape', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:transomics2cytoscape-1.17.0(bioc 3.21)transomics2cytoscape-1.16.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
networksoftwarepathwaysdataimportkegg
Last updated 17 days agofrom:85fc186571. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:create3DnetworkcreateTransomicEdgesec2reactioninstallCyApps
Dependencies:askpassbackportsbase64encbase64urlBiocGenericsBiostringsbitopscaToolsclicrayoncurldigestdplyrevaluatefansifastmapfsgenericsGenomeInfoDbGenomeInfoDbDatagluegplotsgraphgtoolshtmltoolshttrIRangesIRdisplayIRkerneljsonliteKEGGRESTKernSmoothlifecyclemagrittrmimeopensslpbapplypbdZMQpillarpkgconfigpngpurrrR6RColorBrewerRCurlRCy3reprRJSONIOrlangS4VectorsstringisystibbletidyselectUCSC.utilsutf8uuidvctrswithrXMLXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create 3D network view for transomics visualization. | create3Dnetwork |
| Create Trans-Omic edges between layers of the network. | createTransomicEdges |
| Convert KEGG enzyme IDs to KEGG reaction IDs. | ec2reaction |
