Package: GwasDataImport 0.2.1

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_0.2.1.tar.gz
GwasDataImport_0.2.1.zip(r-4.7)GwasDataImport_0.2.1.zip(r-4.6)GwasDataImport_0.2.1.zip(r-4.5)
GwasDataImport_0.2.1.tgz(r-4.6-any)GwasDataImport_0.2.1.tgz(r-4.5-any)
GwasDataImport_0.2.1.tar.gz(r-4.7-any)GwasDataImport_0.2.1.tar.gz(r-4.6-any)
GwasDataImport_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GwasDataImport/json (API)

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

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

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

On CRAN:

Conda:

5.05 score 3 stars 18 scripts 15 exports 91 dependencies

Last updated from:91c27f37aa. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING237
source / vignettesOK293
linux-release-x86_64WARNING214
macos-release-arm64WARNING100
macos-oldrel-arm64WARNING85
windows-develWARNING136
windows-releaseWARNING126
windows-oldrelWARNING131
wasm-releaseOK197

Exports:%>%being_processedcreate_build_referencecreate_martsDatasetdetermine_builddetermine_build_biomartdetermine_build_positiondetermine_new_datasetsebi_datasetsEbiDatasetget_ftp_pathget_positionsliftover_gwaslistftp

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehmshttrhttr2ieugwasrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryaml

Importing datasets into OpenGWAS
As a Contributor | Prerequisites | Summary stats file format | OpenGWAS ID | Setup | Upload a single dataset | 1. Create metadata (two methods) | 1a. Using the web portal | 1b. Using R/GwasDataImport alone | 2. Modify the metadata (only when necessary) | 3. Format the file and upload for QC | 4. Check QC pipeline state and report, and submit for approval | Upload in bulk | What's next | Known issues
Rendered fromimport_pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2020-05-30

Importing datasets into OpenGWAS [DEPRECATED]
1. Download the summary dataset | 2. Initialise | 3. Specify columns in dataset | 4. Input the meta-data | 5. Check that the meta-data are correct | 6. Process the summary dataset | 6. Upload meta-data | 7. Upload processed summary dataset | 8. Wait for the API pipeline to convert to VCF format, annotate and create a report | Summary | Example
Rendered fromimport_pipeline_deprecated.Rmdusingknitr::rmarkdown

Last update: 2026-02-16
Started: 2026-02-16

Automating liftover
Rendered fromliftover.Rmdusingknitr::rmarkdown

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

EBI upload pipeline
Objectives | Complete workflow for one dataset | Running each step individually | Workflow for all datasets | Lookup build | Suhre proteins | EBI Ignore list
Rendered fromebi_workflow.Rmdusingknitr::rmarkdown

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

Edit existing GWAS meta data
Rendered fromedit.Rmdusingknitr::rmarkdown

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

Looking up chromosome and position for large sets of rs IDs
Rendered fromget_positions.Rmdusingknitr::rmarkdown

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

Test run for upload system
Rendered fromtestrun.Rmdusingknitr::rmarkdown

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