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

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'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/oompa

Datasets:

12 exports 0.00 score 12 dependencies 540 downloads

Last updated 4 months agofrom:fbd75f4c3a

Exports:collectAnchorscollectEdgescollectGroupscollectLabelscollectNodescollectShapescycleSubgraphedgeLegendfindCyclesGPMLtoIgraphinterpretCyclenodeLegend

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrsXML

WayFindR: Computing Graph Metrics on WikiPathways

Polina Bombina and Kevin R. Coombes

Rendered fromWayFindR_graphs.Rmdusingknitr::rmarkdownon Jul 10 2024.

Last update: 2024-04-11
Started: 2024-04-11

WayFindR: Creating Graph Structures From WikiPathways Files

Polina Bombina and Kevin R. Coombes

Rendered fromWayFindR_getStarted.Rmdusingknitr::rmarkdownon Jul 10 2024.

Last update: 2024-04-11
Started: 2024-04-11

Readme and manuals

Help Manual

Help pageTopics
Finding Cycles in Biological PathwayscycleSubgraph 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
Converting GPML FIles to Igraph ObjectsedgeLegend GPMLtoIgraph nodeLegend