ReactomeGraph4R

Interface for the Reactome Graph Database

Bioconductor version: Release (3.20)

Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.

Author: Chi-Lam Poon [aut, cre] , Reactome [cph]

Maintainer: Chi-Lam Poon <clpoon807 at gmail.com>

Citation (from within R, enter citation("ReactomeGraph4R")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("ReactomeGraph4R")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GraphAndNetwork, Network, Pathways, Reactome, Software
Version	1.14.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	Apache License (>= 2)
Depends	R (>= 4.1)
Imports	neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table, rlang, ReactomeContentService4R, doParallel, parallel, foreach
System Requirements
URL	https://github.com/reactome/ReactomeGraph4R
Bug Reports	https://github.com/reactome/ReactomeGraph4R/issues

Suggests	knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson
Linking To
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	ReactomeGraph4R_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ReactomeGraph4R
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ReactomeGraph4R
Bioc Package Browser	https://code.bioconductor.org/browse/ReactomeGraph4R/
Package Short Url	https://bioconductor.org/packages/ReactomeGraph4R/
Package Downloads Report	Download Stats