Package: graphite 1.53.0
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-1.53.0(bioc 3.21)graphite-1.52.0(bioc 3.20)
pathwaysthirdpartyclientgraphandnetworknetworkreactomekeggmetabolomicsbioinformaticsmirrorpathway-analysis
Last updated 22 days agofrom:e3017721d0. Checks:OK: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | WARNING | Nov 01 2024 |
| R-4.5-linux | WARNING | Nov 01 2024 |
| R-4.4-win | WARNING | Nov 01 2024 |
| R-4.4-mac | OK | Nov 01 2024 |
| R-4.3-win | WARNING | Nov 01 2024 |
| R-4.3-mac | OK | Nov 01 2024 |
Exports:buildPathwayconvertIdentifierscytoscapePlotedgeDataedgeData<-edgeDataDefaults<-edgesnodespathwayDatabasepathwayDatabasespathwayGraphpathwayIdpathwayspathwaySpeciespathwayTimestamppathwayTitlepathwayURLplotprepareSPIArunSPIArunTopologyGSA
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluegraphhttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpkgconfigplogrpngpurrrR6rappdirsrlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
GRAPH Interaction from pathway Topological Environment
Rendered fromgraphite.Rnwusingutils::Sweaveon Nov 01 2024.Last update: 2023-10-14
Started: 2013-10-22
Pathway Analysis of Metabolic Activities
Rendered frommetabolites.pdf.asisusingR.rsp::asison Nov 01 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 |