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solvebio-r

SolveBio R Bindings

https://github.com/solvebio/solvebio-r

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
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.7%) to scientific vocabulary

Keywords

solvebio

Keywords from Contributors

genomics bioinformatics
Last synced: 11 months ago · JSON representation

Repository

SolveBio R Bindings

Basic Info
  • Host: GitHub
  • Owner: solvebio
  • License: other
  • Language: R
  • Default Branch: master
  • Size: 1.16 MB
Statistics
  • Stars: 4
  • Watchers: 16
  • Forks: 6
  • Open Issues: 23
  • Releases: 10
Topics
solvebio
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

SolveBio for R

This version of SolveBio for R is compatible with Vault-based datasets only (released on July 28th, 2017).

Build Status CRAN\_Status\_Badge

This package contains the SolveBio R language bindings. SolveBio makes it easy to access genomic reference data.

Features of this package include:

  • Authentication with SolveBio's API
  • REST API query support
  • S3 object system for SolveBio API resources
  • Portability between most platforms: Linux, Windows, OS X.

Please see the SolveBio documentation for more information about the platform.

Installation

Installing this package requires an installed R environment.

R install.packages("solvebio") library(solvebio)

Usage

```R

By default it will look for a key in the $SOLVEBIOAPIKEY environment variable.

library(solvebio)

You may also supply an API key in your code

login(api_key="")

RStudio users can put the following line in ~/.Rprofile

Sys.setenv(SOLVEBIOAPIKEY="")

Retrieve a list of all datasets

datasets <- Dataset.all()

Retrieve a specific dataset (metadata)

ClinVar <- Dataset.getbyfull_path("solvebio:public:/ClinVar/3.7.4-2017-01-30/Variants-GRCh37")

Query a dataset with filters as JSON:

filters <- '[["gene_symbol", "BRCA1"]]'

or, filters as R code:

filters <- list(list('genesymbol', 'BRCA1'), list('clinicalsignificance', 'Benign'))

Execute the queries

NOTE: paginate=TRUE may issue multiple requests, depending on the dataset and filters

results <- Dataset.query(id = ClinVar$id, filters = filters, limit = 1000, paginate = TRUE)

Access the results (flattened by default)

results

```

Shiny

To use SolveBio in your Shiny app, refer to the docs on Developing Applications with R Shiny and SolveBio.

This package provides a Shiny server wrapper called solvebio::protectedServer() which requires users to authenticate with SolveBio and authorize the app before proceeding. In addition, you may enable token cookie storage by installing ShinyJS and adding JS code (solvebio::protectedServerJS()) to your Shiny UI.

An example app is available in the solvebio-shiny-example GitHub repository.

Developers

To install the development version of this package from GitHub, you will need the devtools package.

R install.packages(c("devtools", "httr", "jsonlite")) library(devtools) devtools::install_github("solvebio/solvebio-r", ref="master") library(solvebio)

To run the test suite:

bash make test

Packaging and Releasing

  1. Bump the version using the bumpversion command (pip install bumpversion).
  2. Update the NEWS.md with changes.
  3. Update the DESCRIPTION file with the latest date.

  4. Regenerate roxygen2 and build/check the tarball:

    make clean make make check

  5. Submit to CRAN.

Owner

  • Name: SolveBio
  • Login: solvebio
  • Kind: organization
  • Location: New York

GitHub Events

Total
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 3
  • Pull request review event: 1
  • Pull request event: 4
  • Create event: 2
Last Year
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 3
  • Pull request review event: 1
  • Pull request event: 4
  • Create event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 293
  • Total Committers: 17
  • Avg Commits per committer: 17.235
  • Development Distribution Score (DDS): 0.42
Past Year
  • Commits: 2
  • Committers: 2
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
David Caplan d****n@g****m 170
David Caplan d****n@s****m 65
Irina Gershgorin i****a@s****m 18
Stephen Kelly s****m 17
Irina Gershgorin i****a@I****l 4
Nikola Krivacevic 3****5 3
Tatjana Damnjanović t****a@s****m 3
Dandan Xu d****n@s****m 2
Dandan d****u@g****m 2
Jeff Hull j****f@s****m 2
Caplan, David d****n@p****m 1
Jake Feala j****a@h****m 1
David Park d****k@s****m 1
Jeff Hull j****4@g****m 1
Lamarine, Marc m****e@p****m 1
Joseph Huttner j****r@s****m 1
Jeroen Ooms j****s@g****m 1
Committer Domains (Top 20 + Academic)
solvebio.com: 7 precisionformedicine.com: 2 h3biomedicine.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 51
  • Total pull requests: 59
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 5
  • Total pull request authors: 10
  • Average comments per issue: 0.78
  • Average comments per pull request: 0.37
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • davecap (41)
  • iainmwallace (6)
  • jsh2134 (2)
  • dandanxu (1)
  • dragosmg (1)
Pull Request Authors
  • davecap (46)
  • stevekm (4)
  • krivi95 (3)
  • damnjanovictanja (3)
  • igersh (2)
  • tobiguennel (2)
  • jsh2134 (1)
  • jhuttner (1)
  • jeroen (1)
  • davidhpark (1)
Top Labels
Issue Labels
enhancement (18) bug (8) feature (6) documentation (4) needs-input (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 563 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 32
  • Total maintainers: 1
cran.r-project.org: solvebio

The Official SolveBio API Client

  • Versions: 32
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 563 Last month
  • Docker Downloads: 21,613
Rankings
Forks count: 10.1%
Downloads: 23.6%
Stargazers count: 24.2%
Average: 24.6%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
tobi.guennel@precisionformedicine.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • httr * imports
  • jsonlite * imports
  • mime * imports
  • openssl * suggests
  • shiny * suggests
  • shinyjs * suggests
  • testthat * suggests
.github/workflows/r-package.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite