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Some data files and scripts for our oligotyping analysis of human oral microbiota.
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v1v3
v3v5
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README.md
analysis-of-differential-abudance.R
generate-figures.R

README.md

README

We recently published a study in which we analyzed the human oral microbiome data generated by the HMP project. The paper is available online:

http://www.pnas.org/content/111/28/E2875

This repository contains two R scripts and some data files we used to generate results in the paper:

  • analysis-of-differential-abundance.R: This script identifies the site preference of an oligotype in the human oral cavity and reports its significance. Please read the Calculation of Site Preferences section under Material and Methods in our manuscript.
  • generate-figures.R: We used these functions to generate Figures 2, 3, 4 and 5 in the manuscript. If you simply run it, the script will generate three example figures.
  • v1v3 and v3v5 directories contain data files that are used either of these scripts.

Please do not hesitate to get in touch with me if you have any questions.

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