ReactomeGraph4R

DOI: 10.18129/B9.bioc.ReactomeGraph4R  

Interface for the Reactome Graph Database

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GraphAndNetwork, Network, Pathways, Reactome, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Apache License (>= 2)
Depends	R (>= 4.1)
Imports	neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table, rlang, ReactomeContentService4R, doParallel, parallel, foreach
LinkingTo
Suggests	knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson
SystemRequirements
Enhances
URL	https://github.com/reactome/ReactomeGraph4R
BugReports	https://github.com/reactome/ReactomeGraph4R/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ReactomeGraph4R_1.6.0.tar.gz
Windows Binary	ReactomeGraph4R_1.6.0.zip
macOS Binary (x86_64)	ReactomeGraph4R_1.6.0.tgz
macOS Binary (arm64)	ReactomeGraph4R_1.6.0.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