graphite

DOI: 10.18129/B9.bioc.graphite  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see graphite.

GRAPH Interaction from pathway Topological Environment

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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	1.44.0
In Bioconductor since	BioC 2.9 (R-2.14) (11.5 years)
License	AGPL-3
Depends	R (>= 4.2), methods
Imports	AnnotationDbi, graph(>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr
LinkingTo
Suggests	checkmate, 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	https://github.com/sales-lab/graphite
BugReports	https://github.com/sales-lab/graphite/issues
Depends On Me	PoTRA
Imports Me	dce, EnrichmentBrowser, mogsa, multiGSEA, ReactomePA, sSNAPPY, 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_1.44.0.tar.gz
Windows Binary	graphite_1.44.0.zip
macOS Binary (x86_64)	graphite_1.44.0.tgz
macOS Binary (arm64)	graphite_1.44.0.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/
Package Downloads Report	Download Stats