Package: ReactomeGraph4R 1.15.0
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:
ReactomeGraph4R_1.15.0.tar.gz
ReactomeGraph4R_1.15.0.zip(r-4.5)ReactomeGraph4R_1.15.0.zip(r-4.4)ReactomeGraph4R_1.15.0.zip(r-4.3)
ReactomeGraph4R_1.15.0.tgz(r-4.4-any)ReactomeGraph4R_1.15.0.tgz(r-4.3-any)
ReactomeGraph4R_1.15.0.tar.gz(r-4.5-noble)ReactomeGraph4R_1.15.0.tar.gz(r-4.4-noble)
ReactomeGraph4R_1.15.0.tgz(r-4.4-emscripten)ReactomeGraph4R_1.15.0.tgz(r-4.3-emscripten)
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-1.15.0(bioc 3.21)ReactomeGraph4R-1.13.0(bioc 3.20)
dataimportpathwaysreactomenetworkgraphandnetwork
Last updated 23 days agofrom:af9bdb6ea1. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:loginmatchDiseasesmatchHierarchymatchInteractorsmatchObjectmatchPaperObjectsmatchPErolesmatchPrecedingAndFollowingEventsmatchReactionsInPathwaymatchReferralsmultiObjectsunnestListCol
Dependencies:askpassattemptbase64encbslibcachemclicodetoolscommonmarkcpp11crayoncurldata.tabledigestdoParalleldplyrfansifastmapfontawesomeforeachfsgenericsgetPassgluehtmltoolshttpuvhttrigraphiteratorsjquerylibjsonlitelaterlatticelifecyclemagickmagrittrMatrixmemoisemimeneo4ropensslpillarpkgconfigpromisespurrrR6rappdirsRcppReactomeContentService4Rrlangrstudioapisassshinysourcetoolsstringistringrsystibbletidyrtidyselectutf8vctrswithrxtable
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 |
