The Official SolveBio API Client

R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. For more information, visit < https://www.solvebio.com>.


PLEASE NOTE: The SolveBio R Bindings are currently in alpha. The bindings may change frequently so please check back for updates.

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.

Installing this package requires an installed R environment.

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

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

install.packages(c("devtools", "httr", "jsonlite"))
library(devtools)
devtools::install_github("solvebio/solvebio-r")
library(solvebio)
# By default it will look for a key in the $SOLVEBIO_API_KEY environment variable.
require(solvebio)
# You may also supply an API key in your code
login(api_key="<Your SolveBio API key>")
 
# Retrieve a list of all datasets
datasets = Dataset.all()
 
# Retrieve a specific dataset (metadata)
dataset = Dataset.retrieve('ClinVar/Variants')
 
# Query a dataset with filters as JSON:
filters = '[["gene_symbol", "BRCA1"]]'
# or, filters as R code:
filters = list(list('gene_symbol', 'BRCA1'), list('clinical_significance',
'Benign'))
 
# Execute the queries
# NOTE: paginate=TRUE may issue multiple requests, depending on the dataset and filters
results = Dataset.query('ClinVar/3.7.2-2016-08-02/Variants', filters=filters, limit=1000, paginate=TRUE)
# Access the results (flattened by default)
results
 

News

solvebio 0.3.0

  • Adds Dataset.count() and Dataset.facets() methods
  • Adds NEWS.md file

solvebio 0.2.0

  • Adds automatic pagination support to Dataset.query()

solvebio 0.1.0

  • First alpha release, basic SolveBio API support for querying datasets

Reference manual

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install.packages("solvebio")

2.0.2 by David Caplan, a month ago


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


Browse source code at https://github.com/cran/solvebio


Authors: David Caplan


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports httr, jsonlite, dplyr, mime, digest


See at CRAN