Package: graphite 1.58.0
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:
graphite_1.58.0.tar.gz
graphite_1.58.0.zip(r-4.7)graphite_1.58.0.zip(r-4.6)graphite_1.58.0.zip(r-4.5)
graphite_1.58.0.tgz(r-4.6-any)graphite_1.58.0.tgz(r-4.5-any)
graphite_1.58.0.tar.gz(r-4.7-any)graphite_1.58.0.tar.gz(r-4.6-any)
graphite_1.58.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
graphite/json (API)
NEWS
| # Install 'graphite' in R: |
| install.packages('graphite', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sales-lab/graphite/issues
On BioConductor:graphite-1.59.0(bioc 3.24)graphite-1.58.0(bioc 3.23)
pathwaysthirdpartyclientgraphandnetworknetworkreactomekeggmetabolomicsbioinformaticsmirrorpathway-analysis
Last updated from:eca45eaf33 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.
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| linux-devel-x86_64 | OK | 355 | ||
| source / vignettes | OK | 415 | ||
| linux-release-x86_64 | OK | 419 | ||
| macos-release-arm64 | OK | 229 | ||
| macos-oldrel-arm64 | OK | 175 | ||
| windows-devel | OK | 324 | ||
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| wasm-release | OK | 201 |
Exports:buildPathwayconvertIdentifierscytoscapePlotedgeDataedgeData<-edgeDataDefaults<-edgesnodespathwayDatabasepathwayDatabasespathwayGraphpathwayIdpathwayspathwaySpeciespathwayTimestamppathwayTitlepathwayURLplotprepareSPIApurgeCacheV1runClipperrunSPIArunTopologyGSA
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdir.expiryfastmapfilelockgenericsgluegraphhttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfosysvctrsXVector
GRAPH Interaction from pathway Topological Environment
Rendered fromgraphite.Rnwusingutils::Sweaveon May 29 2026.Last update: 2025-10-23
Started: 2013-10-22
Pathway Analysis of Metabolic Activities
Rendered frommetabolites.pdf.asisusingR.rsp::asison May 29 2026.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 |
| Purge Pathway Data Cache (Format v1) | purgeCacheV1 |
| Run a topological analysis on an expression dataset using clipper. | runClipper runClipper,list-method runClipperMulti |
| Run SPIA analysis | runSPIA |
| Run a topological analysis on an expression dataset using topologyGSA. | runTopologyGSA runTopologyGSA,list-method runTopologyGSAMulti |