DOI: 10.18129/B9.bioc.graphite    

GRAPH Interaction from pathway Topological Environment

Bioconductor version: Release (3.8)

Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, PathBank, PharmGKB, Reactome and SMPDB databases.

Author: Gabriele Sales <gabriele.sales at>, Enrica Calura <enrica.calura at>, Chiara Romualdi <chiara.romualdi at>

Maintainer: Gabriele Sales <gabriele.sales at>

Citation (from within R, enter citation("graphite")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("graphite", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script GRAPH Interaction from pathway Topological Environment
PDF metabolites.pdf
PDF   Reference Manual
Text   NEWS


biocViews BioCarta, GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient
Version 1.28.1
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License AGPL-3
Depends R (>= 2.10), methods
Imports AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils
Suggests a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr,, parallel, R.rsp, RCy3, rmarkdown, SPIA(>= 2.2), testthat, topologyGSA (>= 1.4.0)
Depends On Me ToPASeq
Imports Me EnrichmentBrowser, facopy, mogsa, ReactomePA
Suggests Me clipper, signet
Links To Me
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Source Package graphite_1.28.1.tar.gz
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