Package: GwasDataImport 0.1.2

Gibran Hemani

GwasDataImport: Import EBI Data to OpenGWAS

Determine the new EBI data not present in OpenGWAS. Download dataset and import metadata. Upload processed data and metadata to OpenGWAS.

Authors:Gibran Hemani [aut, cre], Philip Haycock [aut], Tom Palmer [aut]

GwasDataImport_0.1.2.tar.gz
GwasDataImport_0.1.2.zip(r-4.5)GwasDataImport_0.1.2.zip(r-4.4)GwasDataImport_0.1.2.zip(r-4.3)
GwasDataImport_0.1.2.tgz(r-4.4-any)GwasDataImport_0.1.2.tgz(r-4.3-any)
GwasDataImport_0.1.2.tar.gz(r-4.5-noble)GwasDataImport_0.1.2.tar.gz(r-4.4-noble)
GwasDataImport_0.1.2.tgz(r-4.4-emscripten)GwasDataImport_0.1.2.tgz(r-4.3-emscripten)
GwasDataImport.pdf |GwasDataImport.html✨
GwasDataImport/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/mrcieu/gwasdataimport/issues

Datasets:

    On CRAN:

    4.37 score 3 stars 13 scripts 15 exports 171 dependencies

    Last updated 2 years agofrom:4981140f4a. Checks:OK: 1 WARNING: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKNov 10 2024
    R-4.5-winWARNINGNov 10 2024
    R-4.5-linuxWARNINGNov 10 2024
    R-4.4-winWARNINGNov 10 2024
    R-4.4-macWARNINGNov 10 2024
    R-4.3-winWARNINGNov 10 2024
    R-4.3-macWARNINGOct 11 2024

    Exports:%>%being_processedcreate_build_referencecreate_martsDatasetdetermine_builddetermine_build_biomartdetermine_build_positiondetermine_new_datasetsebi_datasetsEbiDatasetget_ftp_pathget_positionsliftover_gwaslistftp

    Dependencies:abindAnnotationDbiaskpassassertthatbackportsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbriobroomBSgenomecachemcallrcarcarDataCheckSumStatsclicodetoolscolorspaceconcatenatecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdescdiffobjdigestdoBydplyrevaluatefansifarverfastmapfilelockformatRFormulafsfutile.loggerfutile.optionsgenericsgenetics.binaRiesGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegwasglue2gwasrapiddgwasvcfhighrhmshttrhttr2ieugwasrIRangesisobandjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelme4lubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpingrpkgbuildpkgconfigpkgloadplogrplyrpngpolynompraiseprettyunitsprocessxprogresspspurrrquantregR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrprojrootRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystestthattibbletidyrtidyselecttimechangetriebeardUCSC.utilsurltoolsutf8VariantAnnotationvctrsviridisLitewaldowithrwritexlxfunXMLxml2XVectoryamlzlibbioc

    Automating liftover

    Rendered fromliftover.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2020-06-05

    EBI upload pipeline

    Rendered fromebi_workflow.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2020-05-30

    Edit existing GWAS meta data

    Rendered fromedit.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2020-06-06

    Importing datasets into OpenGWAS

    Rendered fromimport_pipeline.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2020-05-30

    Looking up chromosome and position for large sets of rs IDs

    Rendered fromget_positions.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2021-02-23

    Test run for upload system

    Rendered fromtestrun.Rmdusingknitr::rmarkdownon Nov 10 2024.

    Last update: 2023-05-01
    Started: 2021-02-23