graphite

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see graphite.

GRAPH Interaction from pathway Topological Environment


Bioconductor version: 3.9

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

Author: Gabriele Sales <gabriele.sales at unipd.it>, Enrica Calura <enrica.calura at gmail.com>, Chiara Romualdi <chiara.romualdi at unipd.it>

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

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

Installation

To install this package, start R (version "3.6") 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")
GRAPH Interaction from pathway Topological Environment PDF R Script
metabolites.pdf PDF
Reference Manual PDF
NEWS Text

Details

biocViews BioCarta, GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient
Version 1.30.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License AGPL-3
Depends R (>= 2.10), methods
Imports AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils
System Requirements
URL
See More
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)
Linking To
Enhances
Depends On Me PoTRA, ToPASeq
Imports Me EnrichmentBrowser, mogsa, ReactomePA, StarBioTrek
Suggests Me clipper, signet
Links To Me
Build Report Build Report

Package Archives

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

Source Package graphite_1.30.0.tar.gz
Windows Binary graphite_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) graphite_1.30.0.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
Old Source Packages for BioC 3.9 Source Archive