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Welcome to the David Lab Biostatistics Handbook! This website is intended to supplement the LAD-LAB GitHub organization by providing detailed documentation and step-by-step guidance for lab members running or maintaining the lab's biostatistical scripts and tools. The instructions on this site assume minimal familiarity with R and shell and should be suitable for almost all biostatistical backgrounds.

Warning

This website is a work in progress. Some pages are still being written or updated. Use the Duke/General tabs throughout the site to switch between Duke-specific and institution-agnostic instructions; selecting a tab on any page will switch all pages to that view.

  • Getting Started: How to get set up and familiarize yourself with GitHub, your computing cluster, and shared storage, as well as other lab biostatistics essentials.
  • Creating a Phyloseq: How to create a phyloseq object from sequencing output, as well as information on creating and maintaining human-foods.csv, the trnL and 12Sv5 references, the SQL taxonomy file, and the common names assignment CSV and code.
  • Post-Phyloseq Processing and Analysis: How to process and analyze your phyloseq once it has been created.

To navigate between pages, use the following keyboard shortcuts:

  • P or , allow you to move to the previous page.
  • N or . allow you to move to the next page.
  • F, S, or / allow you to open the search dialog.

Feedback

If you have comments, questions, or feedback, contact Ashish Subramanian at ashish.subramanian@duke.edu.

If you have comments, questions, or feedback, open an issue on the GitHub repository.