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Bioconductor - graphite (development version)

graphite

This is the development version of graphite; for the stable release version, see graphite.

GRAPH Interaction from pathway Topological Environment

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("graphite")

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

Documentation

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

browseVignettes("graphite")
GRAPH Interaction from pathway Topological Environment PDF R Script metabolites.pdf PDF Reference Manual PDF NEWS Text Details biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient Version 1.55.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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 Enhances Depends On Me Imports Me CBNplot, EnrichmentBrowser, MIRit, mogsa, MOSClip, multiGSEA, ReactomePA, sSNAPPY, ICDS, netgsa Suggests Me clipper, InterCellar, metaboliteIDmapping Links To Me Build Report Build Report Package Archives

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

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