Version Information | Introduction | Installation | Workflow | Input files | (Any number of) network files to be layered in 3D space | Layer definition file | A style file of Cytoscape | Trans-omic interaction file | Example | Conversion from EC number to KEGG reaction ID | Example (with more network layers) | References
Package: transomics2cytoscape 1.23.0
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_1.23.0.tar.gz
transomics2cytoscape_1.23.0.zip(r-4.7)transomics2cytoscape_1.23.0.zip(r-4.6)transomics2cytoscape_1.23.0.zip(r-4.5)
transomics2cytoscape_1.23.0.tgz(r-4.6-any)transomics2cytoscape_1.23.0.tgz(r-4.5-any)
transomics2cytoscape_1.23.0.tar.gz(r-4.7-any)transomics2cytoscape_1.23.0.tar.gz(r-4.6-any)
transomics2cytoscape_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
transomics2cytoscape/json (API)
| # Install 'transomics2cytoscape' in R: |
| install.packages('transomics2cytoscape', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:transomics2cytoscape-1.23.0(bioc 3.24)transomics2cytoscape-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
networksoftwarepathwaysdataimportkegg
Last updated from:fdb2f32150. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 157 | ||
| linux-devel-x86_64 | WARNING | 248 | ||
| source / vignettes | OK | 193 | ||
| linux-release-x86_64 | WARNING | 263 | ||
| macos-release-arm64 | WARNING | 199 | ||
| macos-oldrel-arm64 | WARNING | 112 | ||
| windows-devel | WARNING | 155 | ||
| windows-release | WARNING | 77 | ||
| windows-oldrel | WARNING | 123 | ||
| wasm-release | OK | 145 |
Exports:create3DnetworkcreateTransomicEdgesec2reactioninstallCyApps
Dependencies:askpassbackportsbase64encbase64urlBiocGenericsBiostringsbitopscaToolsclicrayoncurldigestdplyrevaluatefastmapfsgenericsgluegplotsgraphgtoolshtmltoolshttrIRangesIRdisplayIRkerneljsonliteKEGGRESTKernSmoothlifecyclemagrittrmimeopensslpbapplypbdZMQpillarpkgconfigpngpurrrR6RColorBrewerRCurlRCy3reprRJSONIOrlangS4VectorsSeqinfostringisystibbletidyselectutf8uuidvctrswithrXMLXVector
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 |
