Package: otargen 1.1.5

otargen: Access Open Target Genetics

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

Authors:Amir Feizi [aut, cre], Kamalika Ray [aut]

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otargen.pdf |otargen.html✨
otargen/json (API)
NEWS

# 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 site:https://amirfeizi.github.io

On CRAN:

Conda:

4.43 score 9 stars 3 scripts 252 downloads 32 exports 84 dependencies

Last updated 6 months agofrom:ecb11adf10. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 14 2025
R-4.5-winOKMar 14 2025
R-4.5-macOKMar 14 2025
R-4.5-linuxOKMar 14 2025
R-4.4-winOKMar 14 2025
R-4.4-macOKMar 14 2025
R-4.4-linuxOKMar 14 2025
R-4.3-winOKMar 14 2025
R-4.3-macOKMar 14 2025

Exports:chemblQueryclinvarQuerycolocalisationsForGenecompGenomicsQuerygeneInfogenesForVariantgeneticConstraintQuerygetLociGenesgwasColocalisationgwasColocalisationForRegiongwasCredibleSetgwasRegionalindexVariantsAndStudiesForTagVariantknownDrugsQuerymanhattanmousePhenotypesQueryoverlapInfoForStudypheWASplot_colocplot_l2gplot_manhattanplot_phewasqtlColocalisationVariantQueryqtlCredibleSetrun_custom_querystudiesAndLeadVariantsForGeneByL2GstudyInfostudyLocus2GeneTablestudyVariantstagVariantsAndStudiesForIndexVarianttopOverlappedStudiesvariantInfo

Dependencies:base64encbslibcachemclicolorspacecpp11crulcurldatawizarddigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggiraphggiraphExtraggplot2ggrepelghqlgluegraphqlgtablehighrhmshtmltoolshtmlwidgetshttpcodeinsightisobandjanitorjquerylibjsonliteknitrlabelinglatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellmycornlmepillarpkgconfigplyrppcorpurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalessjlabelledsjmiscsnakecasestringistringrsystemfontstibbletidyrtidyselecttimechangetinytextriebeardurltoolsutf8uuidvctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Retrieve ChEMBL data for a specified gene and disease.chemblQuery
Retrieve ClinVar data for a specified gene and disease.clinvarQuery
Retrieves Colocalisation Statistics for a Given GenecolocalisationsForGene
Retrieve Comparative Genomics data for a specified gene.compGenomicsQuery
Retrieve gene summary information.geneInfo
Retrieves variant-surrounding genes with calculated statistics for causal gene prioritization.genesForVariant
Retrieve Genetic Constraint data for a specified gene.geneticConstraintQuery
Retrieve summary information of the genes in a locusgetLociGenes
Retrieve calculated GWAS colocalisation datagwasColocalisation
Retrieve GWAS colocalisation data for a genomic region .gwasColocalisationForRegion
Retrieve GWAS credible set datagwasCredibleSet
Retrieve GWAS summary statistics for a genomic region.gwasRegional
Retrieve population-level summary GWAS statistics.indexVariantsAndStudiesForTagVariant
Retrieve Known Drugs data for a specified gene.knownDrugsQuery
Retrieve GWAS summary statistics to create a Manhattan plotmanhattan
Retrieve Mouse Phenotypes data for a specified gene.mousePhenotypesQuery
Retrieves overlap info for a study and a list of studiesoverlapInfoForStudy
Retrieve PheWAS (Phenome Wide Association Studies) data for a variant.pheWAS
Scatter plot of colocalisations for gene and reported traits.plot_coloc
Radar plot for L2G partial scores from 'studiesAndLeadVariantsForGeneByL2G()'plot_l2g
Plot results from 'manhattan()'plot_manhattan
Plot 'PheWAS()' results.plot_phewas
Retrieve QTL colocalisation results of a variantqtlColocalisationVariantQuery
Retrieve calculated QTL summary statistics for credible variant set.qtlCredibleSet
Running custom GraphQL queriesrun_custom_query
Retrieve "locus-to-gene" (L2G) model summary data for a gene.studiesAndLeadVariantsForGeneByL2G
Retrieve study summary information.studyInfo
Retrieve the locus-to-gene (L2G) data table for loci genes.studyLocus2GeneTable
Retrieves all variants for a study.studyVariants
Retrieves tag variants and studies for a given index variant.tagVariantsAndStudiesForIndexVariant
Retrieve top studies having overlap in identified loci.topOverlappedStudies
Retrieves information about a variant.variantInfo