quincunx

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

https://github.com/ramiromagno/quincunx

Keywords

Repository

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

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# quincunx 


[![CRAN status](https://www.r-pkg.org/badges/version/quincunx)](https://CRAN.R-project.org/package=quincunx)
[![R-CMD-check](https://github.com/ramiromagno/quincunx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/quincunx/actions/workflows/R-CMD-check.yaml)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![10.1093/bioinformatics/btab522](https://img.shields.io/badge/doi-10.1093/bioinformatics/btab522-blue.svg)](https://doi.org/10.1093/bioinformatics/btab522)



The goal of `{quincunx}` is to provide programmatic access to the [Polygenic
Score (PGS) Catalog](https://www.pgscatalog.org/), an open resource for
[polygenic scores](https://en.wikipedia.org/wiki/Polygenic_score) and associated
metadata describing their development and respective assessment.

Browse the online documentation at
[rmagno.eu/quincunx](https://rmagno.eu/quincunx/) to get started.

## Installation

Install `{quincunx}` from CRAN:

``` r
# Install from CRAN
install.packages("quincunx")
```

You can instead install the development version with:

``` r
# install.packages("pak")
pak::pak("ramiromagno/quincunx")
```

## Cheatsheet

  

## Citing this work

`{quincunx}` was published in Bioinformatics in 2021: https://doi.org/10.1093/bioinformatics/btab522.

To generate a citation for this publication from within R:

```{r citation}
citation('quincunx')
```

## Citing PGS Catalog publications

Also, please do not forget to cite the authors behind the original studies and
the papers associated with the PGS Catalog project:

- Lambert, S.A., Gil, L., Jupp, S. et al. The Polygenic Score Catalog as an open
database for reproducibility and systematic evaluation. Nat Genet 53, 420–425
(2021). doi:
[10.1038/s41588-021-00783-5](https://doi.org/10.1038/s41588-021-00783-5)
- Wand, H., Lambert, S.A., Tamburro, C. et al. Improving reporting standards for
polygenic scores in risk prediction studies. Nature 591, 211–219 (2021). doi:
[10.1038/s41586-021-03243-6](https://doi.org/10.1038/s41586-021-03243-6)

## Terms of use

Please note that if you use the data provided by the PGS Catalog either directly
or via `{quincunx}` you agree to abide to the [EMBL-EBI Terms of
Use](https://www.ebi.ac.uk/about/terms-of-use/).

## Code of Conduct

Please note that the `{quincunx`} project is released with a [Contributor Code
of Conduct](https://rmagno.eu/quincunx/CODE_OF_CONDUCT.html). By contributing
to this project, you agree to abide by its terms.

## Acknowledgements

This work would have not been possible without the precious feedback from the
[PGS Catalog team](https://www.pgscatalog.org/), particularly [Samuel
Lambert](https://www.ebi.ac.uk/about/people/samuel-lambert) and [Laurent
Gil](https://www.sanger.ac.uk/person/gil-laurent/).

## Package name and hex sticker

The package name `{quincunx}` is another name for [Galton
Board](https://en.wikipedia.org/wiki/Bean_machine), that so nicely exemplifies
the [Central Limit
Theorem](https://en.wikipedia.org/wiki/Central_limit_theorem), which in turn is
a key concept of genetics, namely, [Fisher’s infinitesimal
model](https://doi.org/10.1016/j.tpb.2017.09.003)... which leads us to Polygenic
Scores, the key concept of the PGS Catalog.

The bird in the hex sticker is a *Porphyrio porphyrio*, an emblematic species
native to the Ria Formosa Natural Park, which is a wildlife reserve surrounding
the University of Algarve, where the authors are affiliated.

Owner

GitHub Events

Committers

Last synced: over 2 years ago

Issues and Pull Requests

Last synced: 11 months ago

Packages