Package: ReactomeGraph4R 1.13.0

Chi-Lam Poon

ReactomeGraph4R: Interface for the Reactome Graph Database

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.

Authors:Chi-Lam Poon [aut, cre], Reactome [cph]

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ReactomeGraph4R.pdf |ReactomeGraph4R.html✨
ReactomeGraph4R/json (API)
NEWS

# Install 'ReactomeGraph4R' in R:

install.packages('ReactomeGraph4R', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/reactome/reactomegraph4r/issues

On BioConductor:ReactomeGraph4R-1.13.0(bioc 3.20)ReactomeGraph4R-1.12.0(bioc 3.19)

bioconductor-package

12 exports 0.61 score 63 dependencies

Last updated 2 months agofrom:e6da7e963d

Exports:login matchDiseases matchHierarchy matchInteractors matchObject matchPaperObjects matchPEroles matchPrecedingAndFollowingEvents matchReactionsInPathway matchReferrals multiObjects unnestListCol

Dependencies:askpass attempt base64enc bslib cachem cli codetools commonmark cpp11 crayon curl data.table digest doParallel dplyr fansi fastmap fontawesome foreach fs generics getPass glue htmltools httpuv httr igraph iterators jquerylib jsonlite later lattice lifecycle magick magrittr Matrix memoise mime neo4r openssl pillar pkgconfig promises purrr R6 rappdirs Rcpp ReactomeContentService4R rlang rstudioapi sass shiny sourcetools stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr xtable

ReactomeGraph4R: an R Interface for the Reactome Graph Database

Chi-Lam Poon

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-04-30
Started: 2021-02-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Log in to the local neo4j server	login
MATCH diseases of PhysicalEntity/Reaction/Pathway	matchDiseases
MATCH hierarchy	matchHierarchy
MATCH interactors	matchInteractors
Basic query for database objects	matchObject
MATCH objects related to a paper	matchPaperObjects
MATCH roles of PhysicalEntity	matchPEroles
MATCH the preceding/following Events	matchPrecedingAndFollowingEvents
MATCH Reactions in associated Pathway	matchReactionsInPathway
MATCH biological referrals	matchReferrals
Retrieve multiple Reactome objects	multiObjects
Unnest a column of lists in a dataframe	unnestListCol