The David Lab’s Biostatistics Handbook

A big part of our lab’s mission is to introduce more researchers to FoodSeq so they can apply the technology across a multitude of studies and disciplines. In service of this goal, we’ve created The David Lab Biostatistics Handbook, powered by GitHub, with step-by-step directions for using FoodSeq.

Part open-source repository, part in-depth tutorial, this resource is designed to support the assessment of plant and animal dietary intake directly from human stool samples using DNA metabarcoding with trnL-P6 (UAA) and 12SV5 markers. The David Lab Biostatistics Handbook is suitable for biostatisticians of all backgrounds, provided a basic familiarity with R and shell.

Please note: This handbook is a living document and evolving over time. We appreciate any and all feedback!

Key upcoming changes include:

  • Generalize the instructions on this website for lab-external use

  • Update older files, like Pipeline-to-Phyloseq.Rmd

  • Add pages for common lab tools, like a human read anonymizer and a 16S pipeline

The David Lab Biostatistics Handbook includes the following:

  • An experimental protocol to amplify trnL from DNA extracted from human fecal samples

  • A computational pipeline to analyze high-throughput trnL amplicon-sequencing data

  • A reference database of trnL sequences for food plants used by humans to assign trnL reads to a plant taxon

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