ReactomeGraph4R
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ReactomeGraph4R.
Interface for the Reactome Graph Database
Bioconductor version: 3.19
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("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
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, GraphAndNetwork, Network, Pathways, Reactome, Software |
| Version | 1.12.0 |
| 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 |
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_1.12.0.tar.gz |
| Windows Binary (x86_64) | ReactomeGraph4R_1.12.0.zip |
| macOS Binary (x86_64) | ReactomeGraph4R_1.12.0.tgz |
| macOS Binary (arm64) | ReactomeGraph4R_1.12.0.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 |