Package: WayFindR 0.1.2
Kevin R. Coombes
WayFindR: Computing Graph Structures on WikiPathways
Converts pathways from 'WikiPathways' GPML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).
Authors:
WayFindR_0.1.2.tar.gz
WayFindR_0.1.2.tar.gz(r-4.5-noble)WayFindR_0.1.2.tar.gz(r-4.4-noble)
WayFindR_0.1.2.tgz(r-4.4-emscripten)WayFindR_0.1.2.tgz(r-4.3-emscripten)
WayFindR.pdf |WayFindR.html✨
WayFindR/json (API)
| # Install 'WayFindR' in R: |
| install.packages('WayFindR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
- edgeColors - GPML GraphingR Data
- edgeTypes - GPML GraphingR Data
- nodeColors - GPML GraphingR Data
- nodeShapes - GPML GraphingR Data
Last updated 7 months agofrom:fbd75f4c3a. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 07 2024 |
| R-4.5-linux | NOTE | Nov 07 2024 |
Exports:collectAnchorscollectEdgescollectGroupscollectLabelscollectNodescollectShapescycleSubgraphedgeLegendfindCyclesGPMLtoIgraphinterpretCyclenodeLegend
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrsXML
WayFindR: Computing Graph Metrics on WikiPathways
Rendered fromWayFindR_graphs.Rmdusingknitr::rmarkdownon Nov 07 2024.Last update: 2024-04-11
Started: 2024-04-11
WayFindR: Creating Graph Structures From WikiPathways Files
Rendered fromWayFindR_getStarted.Rmdusingknitr::rmarkdownon Nov 07 2024.Last update: 2024-04-11
Started: 2024-04-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Finding Cycles in Biological Pathways | cycleSubgraph findCycles gpml-cycles interpretCycle |
| GPML GraphingR Data | edgeColors edgeTypes gpml-data nodeColors nodeShapes |
| Utility Functions to Parse GPML FIles | collectAnchors collectEdges collectGroups collectLabels collectNodes collectShapes gpml-utility |
| Converting GPML FIles to Igraph Objects | edgeLegend GPMLtoIgraph nodeLegend |