Package: WayFindR 0.7.1

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). See <doi:10.1093/nargab/lqag051>.

Authors:Kevin R. Coombes [aut, cre], Polina Bombina [aut]

WayFindR_0.7.1.tar.gz
WayFindR_0.7.1.zip(r-4.7-any)WayFindR_0.7.1.zip(r-4.6-any)
WayFindR_0.7.1.tar.gz(r-4.7-any)WayFindR_0.7.1.tar.gz(r-4.6-any)
WayFindR_0.7.1.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'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.07 score 13 scripts 454 downloads 18 exports 67 dependencies

Last updated from:930823d38b. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK302
source / vignettesOK304
linux-releaseOK308
windows-develOK231
windows-releaseOK235
wasm-releaseOK181

Exports:as.graphNELcollectAnchorscollectEdgescollectEntriescollectGroupscollectLabelscollectNodescollectReactionscollectRelationscollectShapescycleSubgraphdiscoverCyclesedgeLegendfindCyclesGPMLtoIgraphinterpretCycleKGMLtoIgraphnodeLegend

Dependencies:askpassBiocGenericsBiostringsbitbit64bootcellrangerclassclicliprcpp11crayoncurldata.tableDescToolse1071ExactexpmforcatsfsgenericsgldgluegraphhavenhmshttrigraphIRangesjsonliteKEGGRESTlatticelifecyclelmommagrittrMASSMatrixmimemvtnormopensslpillarpkgconfigpngprettyunitsprogressproxyR6RcppreadrreadxlrematchRgraphvizrlangrootSolverstudioapiS4VectorsSeqinfosystibbletidyselecttzdbutf8vctrsvroomwithrXMLXVector

WayFindR: Creating Graph Structures From WikiPathways Files
Introduction | Installation | Retrieving data structure from GPML file | Edges | Nodes | Groups | Anchors | Converting Pathways into igraph objects | Bundling the Process | Finding cycles
Rendered fromWayFindR_getStarted.Rmdusingknitr::rmarkdown

Last update: 2026-01-08
Started: 2024-04-11

WayFindR: Computing Graph Metrics on WikiPathways
Introduction | Data Preparation | Computing graph metrics | Degrees and Hubs
Rendered fromWayFindR_metrics.Rmdusingknitr::rmarkdown

Last update: 2025-04-09
Started: 2025-04-09

WayFindR: Displaying WikiPathways
Introduction | Data Preparation | Plots
Rendered fromWayFindR_plots.Rmdusingknitr::rmarkdown

Last update: 2025-04-09
Started: 2025-04-09

Readme and manuals

Help Manual

Help pageTopics
Convert igraph object to Ragraphas.graphNEL
Finding Cycles in Biological PathwayscycleSubgraph discoverCycles findCycles gpml-cycles interpretCycle
GPML GraphingR DataedgeColors edgeTypes gpml-data nodeColors nodeShapes
Utility Functions to Parse GPML FIlescollectAnchors collectEdges collectGroups collectLabels collectNodes collectShapes gpml-utility
Utility Functions to Parse KGML FIlescollectEntries collectReactions collectRelations kgml-utility
Converting GPML FIles to Igraph ObjectsedgeLegend GPMLtoIgraph KGMLtoIgraph nodeLegend