graphite

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

GRAPH Interaction from pathway Topological Environment

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DOI: 10.18129/B9.bioc.graphite

Bioconductor version: Development (3.23)

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

Author: Gabriele Sales [cre] ORCID iD ORCID: 0000-0003-2078-5661 , 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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient

Version 1.57.0

In Bioconductor since BioC 2.9 (R-2.14) (14 years)

License AGPL-3

Depends R (>= 4.2), methods

Imports AnnotationDbi, graph(>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, lifecycle, purrr, dir.expiry

System Requirements

URL https://github.com/sales-lab/graphite

Bug Reports https://github.com/sales-lab/graphite/issues

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)

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.

Source Package graphite_1.57.0.tar.gz

Windows Binary (x86_64) graphite_1.57.0.zip

macOS Binary (x86_64) graphite_1.57.0.tgz

macOS Binary (arm64) graphite_1.57.0.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