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If you use the tools or protocols described here, please cite this handbook using the DOI above.

Welcome to the David Lab FoodSeq 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.
  • Wet Lab Protocols: How to perform the lab's core sequencing workflow, from DNA extraction through running the MiniSeq.
  • 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, use the widget at the bottom of any page or open an issue on the GitHub repository.