graphite

DOI: 10.18129/B9.bioc.graphite    

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

GRAPH Interaction from pathway Topological Environment

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient
Version 1.41.0
In Bioconductor since BioC 2.9 (R-2.14) (10 years)
License AGPL-3
Depends R (>= 4.1), methods
Imports AnnotationDbi, checkmate, graph(>= 1.67.1), httr, rappdirs, stats, utils, graphics
LinkingTo
Suggests a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA(>= 2.2), testthat, topologyGSA (>= 1.4.0)
SystemRequirements
Enhances
URL
Depends On Me PoTRA
Imports Me dce, EnrichmentBrowser, mogsa, multiGSEA, ReactomePA, StarBioTrek
Suggests Me clipper, InterCellar, metaboliteIDmapping
Links To Me
Build Report  

Package Archives

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

Source Package graphite_1.41.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) graphite_1.41.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/graphite
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/graphite
Package Short Url https://bioconductor.org/packages/graphite/
Package Downloads Report Download Stats

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