README.Rmd

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# quincunx <img src='man/figures/logo.svg' align="right" height="139" />

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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 of `{quincunx}` by setting
[Ramiro Magno’s universe](https://ramiromagno.r-universe.dev/) repository:

``` r
options(repos = c(ramiromagno = 'https://ramiromagno.r-universe.dev',
                CRAN = 'https://cloud.r-project.org'))

install.packages('quincunx')
```

## Cheatsheet

<a href="https://github.com/ramiromagno/cheatsheets/blob/master/quincunx/quincunx_cheatsheet.pdf"><img src="https://raw.githubusercontent.com/ramiromagno/cheatsheets/master/quincunx/quincunx_cheatsheet.png" width="615" height="225"/></a>  

## 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.