<commit_before># R Codelabs

* [Data Analysis using Google Genomics](./1000Genomes-BRCA1-analysis)
* [Quality Control using Google Genomics](./PlatinumGenomes-QC)

## Prerequisites

### Required
1. Install the `bigrquery` package
  ```
  install.packages("bigrquery")
  ```
  
1. Create a [BigQuery enabled project](https://console.developers.google.com/flows/enableapi?apiid=bigquery)
   in the Google Developers Console and save the resulting Project ID for later use.

1. Install the GoogleGenomics R package. 
  ```
  source("http://bioconductor.org/biocLite.R") 
  biocLite() 
  options(repos=biocinstallRepos())
  devtools::install_github("googlegenomics/api-client-r")
  library(GoogleGenomics)
  ```
  
1. Follow the first step on https://cloud.google.com/genomics to set up
   credentials for a "Client ID for native application" and download a `client_secrets.json` file.

1. Now use that file to authenticate the GoogleGenomics library:<commit_msg>Update biocLite to skip package updates.<commit_after># R Codelabs

* [Data Analysis using Google Genomics](./1000Genomes-BRCA1-analysis)
* [Quality Control using Google Genomics](./PlatinumGenomes-QC)

## Prerequisites

### Required
1. Install the `bigrquery` package
  ```
  install.packages("bigrquery")
  ```
  
1. Create a [BigQuery enabled project](https://console.developers.google.com/flows/enableapi?apiid=bigquery)
   in the Google Developers Console and save the resulting Project ID for later use.

1. Install the GoogleGenomics R package. 
  ```
  source("http://bioconductor.org/biocLite.R") 
  biocLite(suppressUpdates=TRUE) 
  options(repos=biocinstallRepos())
  devtools::install_github("googlegenomics/api-client-r")
  library(GoogleGenomics)
  ```
  
1. Follow the first step on https://cloud.google.com/genomics to set up
   credentials for a "Client ID for native application" and download a `client_secrets.json` file.

1. Now use that file to authenticate the GoogleGenomics library:
{'fraction_non_alphanumeric': 0.1099236641221374, 'fraction_numerical': 0.010178117048346057, 'mean_word_length': 4.698550724637681, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6903731', 'n_tokens_mistral': 641, 'n_tokens_neox': 597, 'n_words': 174}