graphite

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

GRAPH Interaction from pathway Topological Environment

Bioconductor version: Development (3.24)

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

Author: Gabriele Sales [cre] 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")):

Enrica Calura, Chiara Romualdi. graphite: GRAPH Interaction from pathway Topological Environment. doi:10.18129/B9.bioc.graphite, R package version 1.59.0, https://bioconductor.org/packages/graphite.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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	1.59.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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, netgsa, ReactomePA, SEMgraph, sSNAPPY
Suggests Me	clipper, InterCellar, metaboliteIDmapping
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	graphite_1.59.0.tar.gz
Windows Binary (x86_64)	graphite_1.59.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	graphite_1.59.0.tgz
macOS Binary (sonoma-arm64)	graphite_1.59.0.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