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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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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