Package: graphite 1.51.0
![](https://r-universe.dev/static/nobody.jpg)
Gabriele Sales
graphite: GRAPH Interaction from pathway Topological Environment
Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.
Authors:
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graphite.pdf |graphite.html✨
graphite/json (API)
NEWS
# Install 'graphite' in R: |
install.packages('graphite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sales-lab/graphite/issues
On BioConductor:graphite-1.51.0(bioc 3.20)graphite-1.50.0(bioc 3.19)
Last updated 2 months agofrom:f63b0c72f1
Exports:buildPathwayconvertIdentifierscytoscapePlotedgeDataedgeData<-edgeDataDefaults<-edgesnodespathwayDatabasepathwayDatabasespathwayGraphpathwayIdpathwayspathwaySpeciespathwayTimestamppathwayTitlepathwayURLplotprepareSPIArunSPIArunTopologyGSA
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluegraphhttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpkgconfigplogrpngpurrrR6rappdirsrlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
GRAPH Interaction from pathway Topological Environment
Rendered fromgraphite.Rnw
usingutils::Sweave
on Jun 30 2024.Last update: 2023-10-14
Started: 2013-10-22
Pathway Analysis of Metabolic Activities
Rendered frommetabolites.pdf.asis
usingR.rsp::asis
on Jun 30 2024.Last update: 2018-05-22
Started: 2018-05-22
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Convertion of PathwayLists into lists. | as.list.PathwayList |
Build a Pathway object. | buildPathway |
Convert the node identifiers of a pathway. | convertIdentifiers |
Plot a pathway graph in Cytoscape | cytoscapePlot |
Class '"Pathway"' | convertIdentifiers,Pathway-method edges,Pathway-method nodes,Pathway-method Pathway-class pathwayDatabase pathwayId pathwaySpecies pathwayTimestamp pathwayTitle pathwayURL plot,Pathway,ANY-method runClipper,Pathway-method runTopologyGSA,Pathway-method |
List the available pathway databases. | pathwayDatabases |
Graph representing the topology of a pathway | pathwayGraph |
Class '"PathwayList"' | $,PathwayList-method convertIdentifiers,PathwayList-method length,PathwayList-method names,PathwayList-method PathwayList-class prepareSPIA,PathwayList-method runClipper,PathwayList-method runTopologyGSA,PathwayList-method [,PathwayList-method [[,PathwayList-method |
Retrieve a list of pathways. | pathways |
Class '"Pathways"' | Pathways-class |
Prepare pathway dataset needed by runSPIA. | prepareSPIA prepareSPIA,list-method |
Run SPIA analysis | runSPIA |
Run a topological analysis on an expression dataset using topologyGSA. | runTopologyGSA runTopologyGSA,list-method runTopologyGSAMulti |