Analyzing microbial count data workshop

Owned by John Calder
Last updated: Oct 17, 2020
3 min read

Course materials

The course materials will be updated regularly on Bitbucket throughout the workshop. You can download the repository.

If you’re feeling git savvy, you can clone the repository.

If you’re not feeling git savvy but you want to, check out this fantastic free book: Happy Git and GitHub for the useR.

Schedule Outline

October 8 - Analyzing count data with regression modeling

From 1:20 - 4pm on Zoom

  • Regression models that predict microbial counts

    • Model based methods

      • Dirichlet Multinomial

      • Other model based approaches

    • Available tools

      • Range of regression packages and code

      • In house tools

What you’ll need to be ready for October 8

  • The R packages installed

  • The code and presentations are available on Bitbucket (see above for downloading)

Recording of workshop from October 8:

October 6 - Analyzing count data for differential abundances

From 1 - 4pm on Zoom

  • Using the multinomial and Dirichlet distributions to model count data

  • Assessing differences in microbial proportions

What you’ll need to be ready for October 6

  • The R packages installed

  • The code and presentations are available on Bitbucket (see above for downloading)

Recording of workshop from October 6:

September 17 - Using the Bash shell with Teton

From 1:15 to 4pm on Zoom (we’ll start at 1:15 to make time for everyone to see the Botany seminar talks today)

  • Using the Bash shell on Windows, Mac, or Linux

  • Intro to using Teton

    • Working in an interactive session

    • Submitting jobs

What you’ll need to be ready for Thursday the 17th:

  • Access to Teton

    • See the Word document below under Pre-workshop materials for a guide to log on from Linda van Diepen

    • Please attempt to logon to Teton before we start this section on Thursday

      • If you cannot logon because you do not have a project associated with Teton fill out the form for a new project on your advisor’s behalf. Or if there is a project but you are not a user on that project, request that you be added to the current project.

  • Zoom

  • Run this html file in a browser to follow along

September 15 - Bioinformatics with DADA2

From 1 to 4pm on Zoom

What you’ll need to be ready for Tuesday the 15th:

  • Zoom

  • Be sure you have the R Packages installed

  • Download the R project from Bitbucket here (it’s the same link as above in the course materials). It’s a big one (> 1Gb), but it will make the first day easier

Recording from September 15:

Recording from September 17:

Unfortunately I forgot to press record for the middle of the workshop. I’m sorry - please ask me any questions about material I didn’t record.

Pre-workshop materials

  • R packages to install

  • First time logging to Teton for windows users

    • Follow this document from Linda van Diepen if you use Windows and do not have a way to login to Teton yet

    • If you use MacOS or Linux, the bottom of the document shows you how to login in to Teton using the Terminal

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