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graphite

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

GRAPH Interaction from pathway Topological Environment


Bioconductor version: Development (3.19)

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 "4.4") 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 1.49.0
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
Enhances
Depends On Me
Imports Me CBNplot, dce, EnrichmentBrowser, MIRit, mogsa, multiGSEA, ReactomePA, sSNAPPY, StarBioTrek
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.

Source Package graphite_1.49.0.tar.gz
Windows Binary
macOS Binary (x86_64) graphite_1.49.0.tgz
macOS Binary (arm64)
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