gwasrapidd: an R package to query, download and wrangle GWAS catalog data

Ramiro Magno; Ana-Teresa Maia

doi:10.1093/bioinformatics/btz605

gwasrapidd: an R package to query, download and wrangle GWAS catalog data

Bioinformatics. 2020 Jan 15;36(2):649-650. doi: 10.1093/bioinformatics/btz605.

Authors

Ramiro Magno^{1

2}, Ana-Teresa Maia^{1

2

3}

Affiliations

¹ Centre for Biomedical Research (CBMR).
² Algarve Biomedical Center (ABC).
³ Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro 8005-139, Portugal.

Abstract

Motivation: The National Human Genome Research Institute Catalog of Published Genome-Wide Association Studies (GWAS) Catalog has collected, curated and made available data from over 7100 studies. The recently developed GWAS Catalog representational state transfer (REST) application programming interface (API) is the only method allowing programmatic access to this resource.

Results: Here, we describe gwasrapidd, an R package that provides the first client interface to the GWAS Catalog REST API, representing an important software counterpart to the server-side component. gwasrapidd enables users to quickly retrieve, filter and integrate data with comprehensive bioinformatics analysis tools, which is particularly critical for those looking into functional characterization of risk loci.

Availability and implementation: gwasrapidd is freely available under an MIT License, and can be accessed from https://github.com/ramiromagno/gwasrapidd.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome-Wide Association Study*
Humans
Publications*
Software