ReactomeGraph4R

DOI: 10.18129/B9.bioc.ReactomeGraph4R    

This is the development version of ReactomeGraph4R; for the stable release version, see ReactomeGraph4R.

Interface for the Reactome Graph Database

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/ReactomeGraph4R
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReactomeGraph4R
Package Short Url https://bioconductor.org/packages/ReactomeGraph4R/
Package Downloads Report Download Stats

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