An R package for Google Genomics API queries.
R
Latest commit 07604db May 15, 2016 d.tenenbaum committed with siddharthab Version bump to trigger package rebuilding now that purl()'ing issue
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(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which
the build system was setting. Now it's not set, so these .R files are
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README.rst

GoogleGenomics Build Status

This R client fetches reads and variants data from the Google Genomics API and provides converters to obtain BioConductor S4 classes like GAlignments, and GRanges and VRanges.

Getting started

  • You'll need valid credentials. Follow the sign up instructions. Download the JSON file for the native app or the service account, or note down the Client ID and Client secret values for the native app. If you only want to access public data, you can simply use the public API key.
  • To install the developer version of this package:
source("http://bioconductor.org/biocLite.R")
useDevel(TRUE) # Skip this step if you do not want the devel version.
# Make sure you are using BioConductor version 3.0 from the output of the above steps.

biocLite("GoogleGenomics")
library(GoogleGenomics)

After loading the package, the function authenticate needs to be called once. Alternatively, you can save the public key in the environment variable GOOGLE_API_KEY.

See the following examples for more detail:

Shiny

Inside of the shiny directory, some basic functionality has been turned into a Shiny app. You can view the hosted version of the application on shinyapps.io:

http://googlegenomics.shinyapps.io/reads

See the README for more information.

Project status

Goals

  • Provide an R package that hooks up the Genomics APIs to all of the other great existing R tools for biology. This package should be consumable by R developers.
  • In addition, for non-developers, provide many Read and Variant analysis samples that can easily be run on API data without requiring a lot of prior biology or cs knowledge.

Current status

This project is in active development - the current code is for a minimum viable package. See GitHub issues for more details.