Introduction | Installation | Retrieving data structure from GPML file | Edges | Nodes | Groups | Anchors | Converting Pathways into igraph objects | Bundling the Process | Finding cycles
Package: WayFindR 0.7.0
Kevin R. Coombes
WayFindR: Computing Graph Structures on WikiPathways
Converts pathways from 'WikiPathways' GPML format or 'KEGG' KGML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).
Authors:
WayFindR_0.7.0.tar.gz
WayFindR_0.7.0.tar.gz(r-4.7-any)WayFindR_0.7.0.tar.gz(r-4.6-any)
WayFindR_0.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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
Datasets:
- edgeColors - GPML GraphingR Data
- edgeTypes - GPML GraphingR Data
- nodeColors - GPML GraphingR Data
- nodeShapes - GPML GraphingR Data
Last updated from:ad46ec3feb. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 297 | ||
| source / vignettes | OK | 300 | ||
| linux-release-x86_64 | OK | 304 | ||
| wasm-release | OK | 153 |
Exports:as.graphNELcollectAnchorscollectEdgescollectEntriescollectGroupscollectLabelscollectNodescollectReactionscollectRelationscollectShapescycleSubgraphdiscoverCyclesedgeLegendfindCyclesGPMLtoIgraphinterpretCycleKGMLtoIgraphnodeLegend
Dependencies:askpassBiocGenericsBiostringsbitbit64bootcellrangerclassclicliprcpp11crayoncurldata.tableDescToolse1071ExactexpmforcatsfsgenericsgldgluegraphhavenhmshttrigraphIRangesjsonliteKEGGRESTlatticelifecyclelmommagrittrMASSMatrixmimemvtnormopensslpillarpkgconfigpngprettyunitsprogressproxyR6RcppreadrreadxlrematchRgraphvizrlangrootSolverstudioapiS4VectorsSeqinfosystibbletidyselecttzdbutf8vctrsvroomwithrXMLXVector
WayFindR: Creating Graph Structures From WikiPathways Files
Last update: 2026-01-08
Started: 2024-04-11
WayFindR: Computing Graph Metrics on WikiPathways
Introduction | Data Preparation | Computing graph metrics | Degrees and Hubs
Last update: 2025-04-09
Started: 2025-04-09
WayFindR: Displaying WikiPathways
Introduction | Data Preparation | Plots
Last update: 2025-04-09
Started: 2025-04-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert igraph object to Ragraph | as.graphNEL |
| Finding Cycles in Biological Pathways | cycleSubgraph discoverCycles 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 |
| Utility Functions to Parse KGML FIles | collectEntries collectReactions collectRelations kgml-utility |
| Converting GPML FIles to Igraph Objects | edgeLegend GPMLtoIgraph KGMLtoIgraph nodeLegend |