graphite

GRAPH Interaction from pathway Topological Environment

Bioconductor version: 3.23 · Package version: 1.58.0

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

Installation

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

BiocManager::install("graphite")

Maintainer	Gabriele Sales <gabriele.sales@unipd.it>
Author	Gabriele Sales [cre] (ORCID: <https://orcid.org/0000-0003-2078-5661>), Enrica Calura [aut], Chiara Romualdi [aut]
License	AGPL-3
URL	https://github.com/sales-lab/graphite
Bug Reports	https://github.com/sales-lab/graphite/issues
Downloads rank	5952
Source branch	RELEASE_3_23
biocViews	GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Reactome, Software, ThirdPartyClient

Dependencies

Depends: R (>= 4.2), methods

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

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)

Reverse dependencies

Imports Me (10): CBNplot, EnrichmentBrowser, MIRit, mogsa, MOSClip, multiGSEA, netgsa, ReactomePA, SEMgraph, sSNAPPY

Suggests Me (3): clipper, InterCellar, metaboliteIDmapping