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gwasrapidd

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

https://github.com/ramiromagno/gwasrapidd

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
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  • ○
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  • ○
    Scientific vocabulary similarity
    Low similarity (16.7%) to scientific vocabulary

Keywords

association-studies gwas-catalog human r rest-client snp trait trait-ontology
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 98
  • Watchers: 2
  • Forks: 14
  • Open Issues: 4
  • Releases: 0
Topics
association-studies gwas-catalog human r rest-client snp trait trait-ontology
Created over 7 years ago · Last pushed 9 months ago
Metadata Files
Readme Contributing License Code of conduct

README.Rmd 

---
output: github_document
---



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

# gwasrapidd gwasrapidd website

[![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-CMD-check](https://github.com/ramiromagno/gwasrapidd/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/gwasrapidd/actions/workflows/R-CMD-check.yaml)
[![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:
[doi.org/10.1093/bioinformatics/btz469](https://doi.org/10.1093/bioinformatics/btz469)
- 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).

Owner

  • Name: Ramiro Magno
  • Login: ramiromagno
  • Kind: user
  • Company: Pattern Institute

Data Scientist

GitHub Events

Total
  • Issues event: 8
  • Watch event: 7
  • Issue comment event: 12
  • Push event: 9
Last Year
  • Issues event: 8
  • Watch event: 7
  • Issue comment event: 12
  • Push event: 9

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 376
  • Total Committers: 4
  • Avg Commits per committer: 94.0
  • Development Distribution Score (DDS): 0.008
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ramiro Magno r****o@g****m 373
Pradeep Eranti e****9@g****m 1
Katrin Leinweber k****i@p****e 1
Hadley Wickham h****m@g****m 1
Committer Domains (Top 20 + Academic)
posteo.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 50
  • Total pull requests: 4
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 19 days
  • Total issue authors: 26
  • Total pull request authors: 3
  • Average comments per issue: 3.38
  • Average comments per pull request: 1.25
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 5
  • Pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ramiromagno (15)
  • mightyphil2000 (6)
  • MattCloward (3)
  • Shicheng-Guo (2)
  • jyjo43043ver1 (2)
  • peranti (2)
  • Dicky84 (1)
  • z1242099843 (1)
  • tzup (1)
  • milcs40 (1)
  • jinjinzhou (1)
  • lizlitkowski (1)
  • totajuliusd (1)
  • abhiachoudhary (1)
  • huyou0916 (1)
Pull Request Authors
  • peranti (2)
  • katrinleinweber (1)
  • hadley (1)
Top Labels
Issue Labels
bug (10) question (4) enhancement (4) documentation (3) help wanted (1)
Pull Request Labels
documentation (2)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,014 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 6
  • Total maintainers: 1
cran.r-project.org: gwasrapidd

'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 1,014 Last month
Rankings
Stargazers count: 4.8%
Forks count: 5.5%
Average: 15.3%
Dependent repos count: 16.4%
Downloads: 21.1%
Dependent packages count: 28.6%
Maintainers (1)
rmagno@pattern.institute
Last synced: 6 months ago

Dependencies

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