GoogleGenomics

api-client-r

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

• First you'll need to setup an R environment.
• Then 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")
biocLite() # Make sure you are using BioConductor version 3.0 or above.
options(repos=biocinstallRepos())
install.packages("devtools")
devtools::install_github("googlegenomics/api-client-r")
library(GoogleGenomics)

After loading the package, the function authenticate needs to be called once.

See the following examples for more detail:

• Working with Reads
• Working with Variants
• and also the integration tests

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.