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ReactomeGraph4R

Interface for the Reactome Graph Database


Bioconductor version: Release (3.18)

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 "4.3") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ReactomeGraph4R")
Introduction HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GraphAndNetwork, Network, Pathways, Reactome, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
See More
Suggests knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ReactomeGraph4R_1.10.0.tar.gz
Windows Binary ReactomeGraph4R_1.10.0.zip
macOS Binary (x86_64) ReactomeGraph4R_1.10.0.tgz
macOS Binary (arm64) ReactomeGraph4R_1.10.0.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