Package: R4AOP 0.99.0

Sidra Adil

R4AOP: Access the AOP-Wiki Through Its REST API

Provides functions to retrieve Adverse Outcome Pathways (AOPs), Key Events, Key Event Relationships, stressors, chemicals and genes from the AOP-Wiki through its REST API, without writing SPARQL queries. Each exported function corresponds to one API endpoint, and results are returned as tibbles that fit directly into an R workflow. Pagination, input validation and session caching are handled internally, and every result carries the version of the AOP-Wiki data it came from, so that analyses can be reported reproducibly.

Authors:Sidra Adil [aut, cre], Egon Willighagen [ctb], Tooba Abbassi-Daloii [ctb], Marvin Martens [aut]

R4AOP_0.99.0.tar.gz
R4AOP_0.99.0.zip(r-4.7-any)R4AOP_0.99.0.zip(r-4.6-any)R4AOP_0.99.0.zip(r-4.5-any)
R4AOP_0.99.0.tgz(r-4.6-any)R4AOP_0.99.0.tgz(r-4.5-any)
R4AOP_0.99.0.tar.gz(r-4.7-any)R4AOP_0.99.0.tar.gz(r-4.6-any)
R4AOP_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
R4AOP/json (API)

# Install 'R4AOP' in R:

install.packages('R4AOP', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sidraadil/r4aop/issues

On CRAN:

software thirdpartyclient pathways genesetenrichment annotation dataimport

3.30 score 42 exports 47 dependencies

Last updated from:ab2ef1687b. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	195
linux-devel	OK	178
source / vignettes	OK	242
linux-release	OK	166
macos-release	OK	121
macos-oldrel	OK	106
windows-devel	OK	110
windows-release	OK	117
windows-oldrel	OK	96
wasm-release	OK	141

Exports:ao_list aop_cache_clear aop_chemicals aop_components aop_data_version aop_dataset_info aop_gene_summary aop_genes aop_get aop_kers aop_key_events aop_list aop_methods aop_plot_components aop_plot_genes aop_search aop_stressors aop_summary chemical_aops chemical_get chemical_key_events chemical_list chemical_pathways gene_get gene_list ke_adverse_outcomes ke_aops ke_chemicals ke_components ke_downstream ke_gene_sets ke_get ke_list ke_mies ke_stressors ke_upstream ker_get ker_list mie_list stressor_aops stressor_get stressor_list

Dependencies:annotate AnnotationDbi askpass Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics glue graph GSEABase httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo sys tibble utf8 vctrs withr XML xtable XVector

Exploring liver fibrosis AOPs with R4AOP

Rendered fromliver-fibrosis.Rmdusingknitr::rmarkdown

Last update: 2026-11-02
Started: 2026-11-02

Help page	Topics
List Adverse Outcomes	ao_list
Clear the R4AOP response cache	aop_cache_clear
Chemicals of an AOP	aop_chemicals
Key Event Components of every Key Event in an AOP	aop_components
Data version of a result	aop_data_version
Dataset information	aop_dataset_info
Summarise the genes of an AOP per Key Event	aop_gene_summary
Genes linked to an AOP	aop_genes
Get a single Adverse Outcome Pathway	aop_get
Key Event Relationships of an AOP	aop_kers
Key Events of an AOP	aop_key_events
List Adverse Outcome Pathways	aop_list
Measurement methods used in an AOP	aop_methods
Plot the Key Event Components of an AOP	aop_plot_components
Plot the genes of an AOP per Key Event	aop_plot_genes
Search across AOP-Wiki entities	aop_search
Stressors of an AOP	aop_stressors
Overview of an AOP	aop_summary
AOPs linked to a chemical	chemical_aops
Get a single chemical	chemical_get
Key Events linked to a chemical	chemical_key_events
List or search chemicals	chemical_list
WikiPathways containing a chemical	chemical_pathways
Get a single gene	gene_get
List genes	gene_list
Adverse Outcomes linked to a Key Event	ke_adverse_outcomes
AOPs containing a Key Event	ke_aops
Chemicals of a Key Event	ke_chemicals
Key Event Components of a Key Event	ke_components
Key Events downstream of a Key Event	ke_downstream
Key Event gene sets of an AOP as a GeneSetCollection	ke_gene_sets
Get a single Key Event	ke_get
List Key Events	ke_list
Molecular Initiating Events linked to a Key Event	ke_mies
Stressors of a Key Event	ke_stressors
Key Events upstream of a Key Event	ke_upstream
Get a single Key Event Relationship	ker_get
List Key Event Relationships	ker_list
List Molecular Initiating Events	mie_list
AOPs linked to a stressor, with their adverse outcomes	stressor_aops
Get a single stressor	stressor_get
List stressors	stressor_list

Package: R4AOP 0.99.0

R4AOP: Access the AOP-Wiki Through Its REST API

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