https://github.com/ramiromagno/gwasrapidd

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
https://github.com/ramiromagno/gwasrapidd

association-studies gwas-catalog human r rest-client snp trait trait-ontology

Last synced: 9 days ago
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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

• Host: GitHub
• URL: https://github.com/ramiromagno/gwasrapidd
• Owner: ramiromagno
• License: other
• Created: 2018-10-31T11:55:20.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-12-15T16:36:49.000Z (about 1 year ago)
• Last Synced: 2025-01-16T22:08:51.918Z (16 days ago)
• Topics: association-studies, gwas-catalog, human, r, rest-client, snp, trait, trait-ontology
• Language: R
• Homepage: https://rmagno.eu/gwasrapidd/
• Size: 19.9 MB
• Stars: 95
• Watchers: 4
• Forks: 14
• Open Issues: 5
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r setup, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  # comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# gwasrapidd 

[![CRAN status](https://www.r-pkg.org/badges/version/gwasrapidd)](https://CRAN.R-project.org/package=gwasrapidd)

[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btz605-blue.svg)](https://doi.org/10.1093/bioinformatics/btz605)

[![](https://img.shields.io/badge/Altmetric-38-yellow.svg)](https://www.altmetric.com/details/64505748)

[![R build status](https://github.com/ramiromagno/gwasrapidd/workflows/R-CMD-check/badge.svg)](https://github.com/ramiromagno/gwasrapidd/actions)

[![Codecov test coverage](https://codecov.io/gh/ramiromagno/gwasrapidd/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ramiromagno/gwasrapidd?branch=master)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)

The goal of `{gwasrapidd}` is to provide programmatic access to the [NHGRI-EBI

Catalog](https://www.ebi.ac.uk/gwas) of published genome-wide association

studies.

Get started by reading the

[documentation](https://rmagno.eu/gwasrapidd/articles/gwasrapidd.html).

## Installation

Install `{gwasrapidd}` from CRAN:

``` r

install.packages("gwasrapidd")

```

## Cheatsheet



## Example

Get studies related to triple-negative breast cancer:

```{r example1}

library(gwasrapidd)

studies <- get_studies(efo_trait = 'triple-negative breast cancer')

studies@studies[1:4]

```

Find associated variants with study `r studies@studies$study_id[1]`:

```{r example2}

variants <- get_variants(study_id = 'GCST002305')

variants@variants[c('variant_id', 'functional_class')]

```

## Citing this work

`{gwasrapidd}` was published in Bioinformatics in 2019:

https://doi.org/10.1093/bioinformatics/btz605.

To generate a citation for this publication from within R:

```{r citation}

citation('gwasrapidd')

```

## Code of Conduct

  

Please note that the `{gwasrapidd}` project is released with a [Contributor Code

of Conduct](https://rmagno.eu/gwasrapidd/CODE_OF_CONDUCT.html). By contributing

to this project, you agree to abide by its terms.

## Similar projects

- Bioconductor R package *gwascat* by Vincent J Carey:

[https://www.bioconductor.org/packages/release/bioc/html/gwascat.html](https://www.bioconductor.org/packages/release/bioc/html/gwascat.html)

- Web application *PhenoScanner V2* by Mihir A. Kamat, James R. Staley, and

others:

[http://www.phenoscanner.medschl.cam.ac.uk/](http://www.phenoscanner.medschl.cam.ac.uk/)

- Web application *GWEHS: Genome-Wide Effect sizes and Heritability Screener* by

Eugenio López-Cortegano and Armando Caballero:

[http://gwehs.uvigo.es/](http://gwehs.uvigo.es/)

## Acknowledgements

This work would have not been possible without the precious help from the GWAS

Catalog team, particularly [Daniel

Suveges](https://www.ebi.ac.uk/about/people/daniel-suveges).