graphite
GRAPH Interaction from pathway Topological Environment
Bioconductor version: Release (3.20)
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")
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 | R Script | |
| metabolites.pdf | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 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, 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_1.52.0.tar.gz |
| Windows Binary (x86_64) | graphite_1.52.0.zip (64-bit only) |
| macOS Binary (x86_64) | graphite_1.52.0.tgz |
| macOS Binary (arm64) | graphite_1.52.0.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 |