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rsnps

Wrapper to a number of SNP web APIs

https://github.com/ropensci/rsnps

Science Score: 20.0%

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
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 11 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.1%) to scientific vocabulary

Keywords

data r r-package rstats snps web-api

Keywords from Contributors

genomics geocode crossref-api doi rmarkdown tidy-data species disease-networks helminth parasites
Last synced: 6 months ago · JSON representation

Repository

Wrapper to a number of SNP web APIs

Basic Info
Statistics
  • Stars: 51
  • Watchers: 8
  • Forks: 22
  • Open Issues: 13
  • Releases: 8
Topics
data r r-package rstats snps web-api
Created about 14 years ago · Last pushed about 2 years ago
Metadata Files
Readme Contributing License

README.Rmd 

---
output: github_document
---


rsnps
=====

```{r, eval=TRUE, echo=FALSE}
knitr::opts_chunk$set(
  warning=FALSE,
  message=FALSE,
  comment="#>"
)
```


[![R build status](https://github.com/ropensci/rsnps/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/rsnps/actions)
[![Build status](https://ci.appveyor.com/api/projects/status/d2lv98726u6t9ut5/branch/master)](https://ci.appveyor.com/project/sckott/rsnps/branch/master/)
[![Codecov test coverage](https://codecov.io/gh/ropensci/rsnps/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rsnps?branch=master)
[![cran version](https://www.r-pkg.org/badges/version/rsnps)](https://cran.r-project.org/package=rsnps)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rsnps?color=E664A4)](https://github.com/r-hub/cranlogs.app)


This package gives you access to data from OpenSNP and NCBI's dbSNP SNP database.

## NOTE

`rsnps` used to be `ropensnp`


## Data sources

This set of functions/package accesses data from:

+ openSNP.org
	+ 
	+ See documentation on the openSNP API 
	+ See blog post about their API 
	+ Relevant functions:
		+ `allgensnp()`, `allphenotypes()`, `annotations()`, `download_users()`, 
		`fetch_genotypes()`, `genotypes()`, `phenotypes()`, `phenotypes_byid()`, `users()`

+ NCBI's dbSNP SNP database
	+ See  for more details
	+ Relevant function:
		+ `ncbi_snp_query()`

## Install

Install from CRAN

```{r eval=FALSE}
install.packages("rsnps")
```

Or dev version

```{r eval=FALSE}
install.packages("remotes")
remotes::install_github("ropensci/rsnps")
```

```{r}
library("rsnps")
```

## Usage

### NCBI dbSNP data

```{r}
snps <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(snps)
```

The `ncbi_snp_query()` function can be used with an NCBI API which gives access 
higher numbers of API requests per second. More information about setting this 
up can be found in the package help accessed via `?rsnps`. 

### openSNP data

`genotypes()` function

```{r}
genotypes('rs9939609', userid='1,6,8', df=TRUE)
```

`phenotypes()` function

```{r}
out <- phenotypes(userid=1)
out$phenotypes$`Hair Type`
```

For more detail, see the [vignette: rsnps tutorial](https://github.com/ropensci/rsnps/tree/master/vignettes).

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/rsnps/issues/).
* License: MIT
* Get citation information for `rsnsps` in R doing `citation(package = 'rsnps')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

[![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

Owner

  • Name: rOpenSci
  • Login: ropensci
  • Kind: organization
  • Email: info@ropensci.org
  • Location: Berkeley, CA

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 373
  • Total Committers: 11
  • Avg Commits per committer: 33.909
  • Development Distribution Score (DDS): 0.56
Past Year
  • Commits: 31
  • Committers: 1
  • Avg Commits per committer: 31.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Scott Chamberlain m****s@g****m 164
Sina Rueger s****r@g****m 120
Julia Gustavsen j****n@g****m 65
Julia Gustavsen j****n@g****m 8
Kevin Ushey k****y@g****m 4
Hao Zhu h****u@h****u 3
Karthik Ram k****m@g****m 3
Ramiro Magno r****t@g****m 2
Sina Rüeger s****r 2
rOpenSci Bot m****t@g****m 1
Hao Zhu h****3@g****m 1
Committer Domains (Top 20 + Academic)
hsl.harvard.edu: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 46
  • Total pull requests: 60
  • Average time to close issues: 9 months
  • Average time to close pull requests: 24 days
  • Total issue authors: 13
  • Total pull request authors: 3
  • Average comments per issue: 2.91
  • Average comments per pull request: 2.12
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 12
  • Average time to close issues: 24 days
  • Average time to close pull requests: 12 days
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 2.2
  • Average comments per pull request: 0.08
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jooolia (22)
  • sinarueeger (11)
  • sckott (2)
  • Mahantesh-Biradar (2)
  • LanyingWei (1)
  • mxw010 (1)
  • Sububioinfo (1)
  • ellisifnygaard (1)
  • nokimchen (1)
  • wigge206 (1)
  • scienception (1)
  • Louwai1 (1)
  • ramiromagno (1)
  • VitorAguiar (1)
  • Abiologist (1)
Pull Request Authors
  • jooolia (32)
  • sinarueeger (27)
  • cruzpazv (1)
Top Labels
Issue Labels
Feature (16) Bug (11) Release (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 485 last-month
  • Total docker downloads: 108,976
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: rsnps

Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 485 Last month
  • Docker Downloads: 108,976
Rankings
Forks count: 3.6%
Stargazers count: 7.1%
Dependent repos count: 13.5%
Average: 15.6%
Downloads: 25.0%
Dependent packages count: 29.1%
Maintainers (1)
j.gustavsen@gmail.com
Last synced: almost 2 years ago
conda-forge.org: r-rsnps
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 33.2%
Dependent repos count: 34.0%
Stargazers count: 37.7%
Average: 39.0%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • crul >= 0.5.2 imports
  • data.table * imports
  • httr * imports
  • jsonlite * imports
  • plyr * imports
  • stringr * imports
  • knitr * suggests
  • markdown * suggests
  • testthat * suggests
  • tibble * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite