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GRAPH Interaction from pathway Topological Environment

Bioconductor version: Release (3.18)

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

Author: Gabriele Sales [cre], Enrica Calura [aut], Chiara Romualdi [aut]

Maintainer: Gabriele Sales <gabriele.sales at unipd.it>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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:

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


biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License AGPL-3
Depends R (>= 4.2), methods
Imports AnnotationDbi, graph(>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr
System Requirements
URL https://github.com/sales-lab/graphite
Bug Reports https://github.com/sales-lab/graphite/issues
See More
Suggests checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA(>= 2.2), testthat, topologyGSA (>= 1.4.0)
Linking To
Depends On Me
Imports Me CBNplot, dce, EnrichmentBrowser, mogsa, multiGSEA, ReactomePA, sSNAPPY, StarBioTrek
Suggests Me clipper, InterCellar, metaboliteIDmapping
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package graphite_1.48.0.tar.gz
Windows Binary graphite_1.48.0.zip
macOS Binary (x86_64) graphite_1.48.0.tgz
macOS Binary (arm64) graphite_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/graphite
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/graphite
Bioc Package Browser https://code.bioconductor.org/browse/graphite/
Package Short Url https://bioconductor.org/packages/graphite/
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