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ReactomeGraph4R

Interface for the Reactome Graph Database

Bioconductor version: Release (3.17)

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 1.8.0
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
Linking To
Suggests knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson
System Requirements
Enhances
URL https://github.com/reactome/ReactomeGraph4R
Bug Reports https://github.com/reactome/ReactomeGraph4R/issues
See More
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_1.8.0.tar.gz
Windows Binary ReactomeGraph4R_1.8.0.zip
macOS Binary (x86_64) ReactomeGraph4R_1.8.0.tgz
macOS Binary (arm64) ReactomeGraph4R_1.8.0.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