quincunx: an R package to query, download and wrangle PGS Catalog data

Ramiro Magno; Isabel Duarte; Ana-Teresa Maia

doi:10.1093/bioinformatics/btab522

quincunx: an R package to query, download and wrangle PGS Catalog data

Bioinformatics. 2021 Dec 22;38(1):294-296. doi: 10.1093/bioinformatics/btab522.

Authors

Ramiro Magno^{1

2}, Isabel Duarte^{1

2}, Ana-Teresa Maia^{1

2

3}

Affiliations

¹ Center for Research in Health Technologies and Information Systems (CINTESIS-UAlg), University of Algarve, Faro 8005-139, Portugal.
² Algarve Biomedical Center (ABC), University of Algarve, Faro 8005-139, Portugal.
³ Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro 8005-139, Portugal.

Abstract

Motivation: The Polygenic Score (PGS) Catalog is a recently established open database of published polygenic scores that, to date, has collected, curated and made available 721 polygenic scores from over 133 publications. The PGS Catalog REST API is the only method allowing programmatic access to this resource.

Results: Here, we describe quincunx, an R package that provides the first client interface to the PGS Catalog REST API. quincunx enables users to query and quickly retrieve, filter and integrate metadata associated with polygenic scores, as well as polygenic scoring files in tidy table format.

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

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

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

MeSH terms

Databases, Factual
Humans
Metadata*
Publications
Software*