For tool creators to share their inventions that analyze, visualize, and make meaning of microbiome data.
Python R
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build/lib/ubiome v0.6.5 bug fixes Jun 28, 2016
dist v0.6.5 bug fixes Jun 28, 2016
.gitignore updated slightly, before merge Jan 28, 2016 New Python article explains python tools with an example. Aug 15, 2016
setup.cfg v0.6.5 bug fixes Jun 28, 2016
uBiomeCompare.R Combine two runs into a single fastq Oct 1, 2015 Example of using utilities Jul 30, 2015

uBiome Tools Repository

Please add your tools here, and edit this file to keep a directory of scripts, programs, templates, or anything else you find useful for manipulating or analyzing uBiome information.

If you are new to uBiome taxonomy files, read our Getting Started document


How to Analyze Your uBiome Results in Python Python module Compare any two uBiome samples to find unique taxa (bacteria) or to show the difference in counts. If you have a Mac, the script works without installing anything else.


RuBiome: simple scripts in R

  • 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.


uBiome JSON to D3 Tree Graph A lightweight JavaScript library that generates an interactive D3 tree visualization from your uBiome JSON data.