Package: otargen 2.1.0

otargen: Access Open Target

Interact seamlessly with Open Target GraphQL endpoint to query and retrieve tidy data tables, facilitating the analysis of gene, disease, drug, and genetic data. For more information about the Open Target API (<https://platform.opentargets.org/api>).

Authors:Amir Feizi [aut, cre]

otargen_2.1.0.tar.gz
otargen_2.1.0.zip(r-4.7-any)otargen_2.1.0.zip(r-4.6-any)otargen_2.1.0.zip(r-4.5-any)
otargen_2.1.0.tgz(r-4.6-any)otargen_2.1.0.tgz(r-4.5-any)
otargen_2.1.0.tar.gz(r-4.7-any)otargen_2.1.0.tar.gz(r-4.6-any)
otargen_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
otargen/json (API)

# Install 'otargen' in R:
install.packages('otargen', repos = c('https://amirfeizi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/amirfeizi/otargen/issues

Pkgdown/docs site:https://amirfeizi.github.io

On CRAN:

Conda:

bioinformatics-toolcomputational-biologygeneitcsopen-target

4.41 score 15 stars 17 scripts 348 downloads 41 exports 43 dependencies

Last updated from:03adb94902. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK125
source / vignettesOK161
linux-releaseOK130
macos-releaseOK190
macos-oldrelOK196
windows-develOK91
windows-releaseOK91
windows-oldrelOK88
wasm-releaseOK99

Exports:adverseEventsQuerychemblQueryclinVarQuerycompGenomicsQuerydepMapQueryeuropePMCQuerygeneBurdenQuerygeneOntologyQuerygeneticConstraintQuerygenomicsEnglandQuerygwasColocalisationgwasCredibleSetgwasCredibleSetsQueryhallmarksQueryindicationsQueryinteractionsQueryknownDrugsChemblQueryknownDrugsGeneQuerylocus2GeneQuerymechanismsOfActionQuerymousePhenotypesQueryorphanetQueryoverlapInfoForStudypathwaysQuerypharmacogenomicsChemblQuerypharmacogenomicsGeneQuerypharmacogenomicsVariantQueryplot_adverse_eventsplot_colocalisationplot_indicationsplot_interactionsplot_l2gqtlCredibleSetsQuerysafetyQuerysharedTraitStudiesQuerytargetLiabilityuniprotLiteratureQueryuniProtVariantsQueryvariantEffectPredictorQueryvariantEffectQueryvariantsQuery

Dependencies:askpassclicpp11crulcurldplyrfarvergenericsggplot2ghqlgluegraphqlgtablehttpcodehttrisobandjsonlitelabelinglifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalesstringistringrsystibbletidyrtidyselecttriebeardurltoolsutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Retrieve Adverse Events data for a specified drug.adverseEventsQuery
Retrieve ChEMBL data for a specified gene and disease.chemblQuery
Retrieve ClinVar data for a specified gene and disease.clinVarQuery
Retrieve Comparative Genomics data for a specified gene.compGenomicsQuery
Retrieve DepMap Essentiality data for a specified gene.depMapQuery
Retrieve Europe PMC data for a specified gene and disease.europePMCQuery
Retrieve Gene Burden data for a specified gene and disease.geneBurdenQuery
Retrieve Gene Ontology data for a specified gene.geneOntologyQuery
Retrieve Genetic Constraint data for a specified gene.geneticConstraintQuery
Retrieve Genomics England data for a specified gene and disease.genomicsEnglandQuery
Retrieve calculated GWAS colocalisation datagwasColocalisation
Retrieve GWAS credible set datagwasCredibleSet
Retrieve GWAS Credible Sets data for a specified target and disease.gwasCredibleSetsQuery
Retrieve Cancer Hallmarks data for a specified gene.hallmarksQuery
Retrieve Indications data for a specified drug.indicationsQuery
Retrieve Interactions data for a specified gene.interactionsQuery
Retrieve indications and clinical report data for a specified drug.knownDrugsChemblQuery
Retrieve drug and clinical candidate data for a specified gene.knownDrugsGeneQuery
Retrieve Locus-to-Gene Predictions data for a specified study locus.locus2GeneQuery
Retrieve Mechanisms of Action data for a specified drug.mechanismsOfActionQuery
Retrieve Mouse Phenotypes data for a specified gene.mousePhenotypesQuery
Retrieve Orphanet data for a specified gene and disease.orphanetQuery
Retrieves overlap info for a study and a list of studiesoverlapInfoForStudy
Retrieve Pathways data for a specified gene.pathwaysQuery
Retrieve Pharmacogenomics data for a specified drug.pharmacogenomicsChemblQuery
Retrieve Pharmacogenomics data for a specified gene.pharmacogenomicsGeneQuery
Retrieve Pharmacogenomics data for a specified variant.pharmacogenomicsVariantQuery
Plot adverse events for a drug as a lollipop chart.plot_adverse_events
Plot GWAS colocalisation results.plot_colocalisation
Plot drug indications by clinical stage.plot_indications
Plot protein interaction network for a gene.plot_interactions
Plot locus-to-gene prediction scores.plot_l2g
Retrieve QTL Credible Sets data for a specified variant.qtlCredibleSetsQuery
Retrieve Safety Liabilities data for a specified gene.safetyQuery
Retrieve Shared Trait Studies data for specified diseases.sharedTraitStudiesQuery
Score a target's safety liability for inhibition or knockout.targetLiability
Retrieve UniProt Literature data for a specified gene and disease.uniprotLiteratureQuery
Retrieve UniProt Variants data for a specified variant.uniProtVariantsQuery
Retrieve Variant Effect Predictor data for a specified variant.variantEffectPredictorQuery
Retrieve Variant Effect data for a specified variant.variantEffectQuery
Retrieve Variants data for a specified study locus.variantsQuery