Tidy R interface to the Open Targets Platform GraphQL API.
Query genes, diseases, drugs, variants, and genetic evidence directly from R and receive analysis-ready tibbles — no manual JSON wrangling required.
CRAN (stable)
install.packages("otargen")GitHub (development)
# install.packages("devtools")
devtools::install_github("amirfeizi/otargen")Every function takes a single identifier (gene, disease, drug, or variant) and returns a tidy tibble.
library(otargen)
# Adverse events reported for imatinib
adverseEventsQuery(chemblId = "CHEMBL941")
# Mechanism of action for imatinib
mechanismsOfActionQuery(chemblId = "CHEMBL941")
# Drug indications with clinical stage info
indicationsQuery(chemblId = "CHEMBL941")# Known drugs and clinical candidates targeting TP53
knownDrugsGeneQuery(ensgId = "ENSG00000141510")
# Cancer hallmarks for TP53
hallmarksQuery(ensgId = "ENSG00000141510")
# Protein-protein interactions for TP53
interactionsQuery(ensgId = "ENSG00000141510", size = 25)
# DepMap cancer cell-line essentiality for EGFR
depMapQuery(ensgId = "ENSG00000146648")
# Target safety liabilities for EGFR
safetyQuery(ensgId = "ENSG00000146648")# ChEMBL evidence linking PARP1 to breast cancer
chemblQuery(ensemblId = "ENSG00000143799", efoId = "EFO_0000305")
# GWAS credible sets for PCSK9 and hyperlipidemia
gwasCredibleSetsQuery(ensemblId = "ENSG00000169174", efoId = "EFO_0004911")
# ClinVar evidence for BRCA1 and ovarian cancer
clinVarQuery(ensemblId = "ENSG00000012048", efoId = "EFO_0001075")
# Literature evidence from Europe PMC
europePMCQuery(ensemblId = "ENSG00000012048", efoId = "EFO_0001075")# Pharmacogenomics data for a drug
pharmacogenomicsChemblQuery(chemblId = "CHEMBL1016")
# UniProt variants
uniProtVariantsQuery(variantId = "4_1804392_G_A")
# Variant effect predictions
variantEffectPredictorQuery(variantId = "1_154453788_C_T")# Locus-to-gene predictions for a credible set
locus2GeneQuery(studyLocusId = "fa375739ca2a6b825ce5cc69d117e84b")
# GWAS colocalisation analysis
gwasColocalisation(study_locus_id = "5a86bfd40d2ebecf6ce97bbe8a737512")| Category | Functions |
|---|---|
| Drug queries | adverseEventsQuery, indicationsQuery,
knownDrugsChemblQuery,
mechanismsOfActionQuery,
pharmacogenomicsChemblQuery |
| Gene / target queries | compGenomicsQuery, depMapQuery,
geneOntologyQuery, geneticConstraintQuery,
hallmarksQuery, interactionsQuery,
knownDrugsGeneQuery, mousePhenotypesQuery,
pathwaysQuery, pharmacogenomicsGeneQuery,
safetyQuery |
| Gene + disease evidence | chemblQuery, clinVarQuery,
europePMCQuery, geneBurdenQuery,
genomicsEnglandQuery, orphanetQuery,
uniprotLiteratureQuery |
| Variant queries | pharmacogenomicsVariantQuery,
uniProtVariantsQuery,
variantEffectPredictorQuery,
variantEffectQuery, variantsQuery |
| Genetics / GWAS | gwasColocalisation, gwasCredibleSet,
gwasCredibleSetsQuery, locus2GeneQuery,
overlapInfoForStudy, qtlCredibleSetsQuery,
sharedTraitStudiesQuery |
Full documentation: https://amirfeizi.github.io/otargen/
Bug fixes for HTTP 400 errors caused by upstream Open Targets API
schema changes. Nine functions updated: chemblQuery,
clinVarQuery, geneBurdenQuery,
orphanetQuery, indicationsQuery,
knownDrugsChemblQuery, knownDrugsGeneQuery,
geneOntologyQuery, and interactionsQuery. See
NEWS.md for details.
If you use otargen in your research, please cite:
Feizi A, Ray D (2023). otargen: an R package for accessing and visualizing Open Targets Genetics data. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad441
Bug reports and feature requests: GitHub Issues
Contributions are welcome via pull requests on GitHub.
MIT