Package: GwasDataImport 0.2

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_0.2.tar.gz
GwasDataImport_0.2.zip(r-4.5)GwasDataImport_0.2.zip(r-4.4)GwasDataImport_0.2.zip(r-4.3)
GwasDataImport_0.2.tgz(r-4.4-any)GwasDataImport_0.1.2.tgz(r-4.3-any)
GwasDataImport_0.2.tar.gz(r-4.5-noble)GwasDataImport_0.2.tar.gz(r-4.4-noble)
GwasDataImport_0.2.tgz(r-4.4-emscripten)GwasDataImport_0.2.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'))

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

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

On CRAN:

5.12 score 3 stars 14 scripts 15 exports 93 dependencies

Last updated 1 months agofrom:03fbe09087. Checks:1 OK, 5 WARNING, 1 FAILURE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 08 2025
R-4.5-win	WARNING	Jan 08 2025
R-4.5-linux	WARNING	Jan 08 2025
R-4.4-win	WARNING	Jan 08 2025
R-4.4-mac	WARNING	Jan 08 2025
R-4.3-win	WARNING	Dec 09 2024
R-4.3-mac	OUTDATED	Oct 11 2024

Exports:%>%being_processed create_build_reference create_marts Dataset determine_build determine_build_biomart determine_build_position determine_new_datasets ebi_datasets EbiDataset get_ftp_path get_positions liftover_gwas listftp

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue hms httr httr2 ieugwasr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML xml2 XVector yaml zlibbioc

Automating liftover

Rendered fromliftover.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

EBI upload pipeline

Rendered fromebi_workflow.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Edit existing GWAS meta data

Rendered fromedit.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Importing datasets into OpenGWAS

Rendered fromimport_pipeline.Rmdusingknitr::rmarkdownon Jan 08 2025.

Last update: 2024-12-08
Started: 2020-05-30

Importing datasets into OpenGWAS [NEW WORKFLOW]

Rendered fromimport_pipeline_new.Rmdusingknitr::rmarkdownon Jan 08 2025.

Last update: 2024-12-09
Started: 2024-12-08

Looking up chromosome and position for large sets of rs IDs

Rendered fromget_positions.Rmdusingknitr::rmarkdownon Jan 08 2025.

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

Test run for upload system

Rendered fromtestrun.Rmdusingknitr::rmarkdownon Jan 08 2025.