useful tools for manipulating uBiome information
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Blog Post uBiome Sleep Update.Rmd
Blog Post uBiome Sleep.Rmd
ecompare.csv Updated documentation Feb 2, 2015
uBiome Jan2015 Analysis.Rmd


These repo contains source code and documentation that I've found useful in managing my uBiome results.

This is not the official uBiome repo, nor is anything here endorsed by uBiome.

The official uBiome repo is here:

Everything else below is here for legacy reasons. Please ignore!

Before you begin, you will need:

  1. An account with
  2. Access to R, the (free) open source scientific programming language, available for Mac/Windows/Unix.


Check out the Beginners Guide (better yet, check the Hackers Guide)

Download the RuBiome source files and copy to the directory of your choice.

Fire up R and run the program uBiome.R to set the correct working directories.

Bacteria to watch

I use this Excel file to analyze each of my samples.

Divided into "good" vs. "bad", though that is probably an imprecise distinction. Nevertheless it may be useful to watch these particular organisms when you are starting.

uBiome Tools

useful tools for manipulating uBiome information

uBiome_compare_samples Given two samples, output all the differences, including the difference in count_norm

uBiome_sample_unique Given two samples, output which rows are the uniquely found in one but not the other.

convert_json_files_to_csv Convert all JSON files in a directory to CSV files, suitable for reading in Excel or use with the other functions here.