This lesson is still being designed and assembled (Pre-Alpha version)

Microbiota data analysis: Welcome!

Welcome!

This tutorial will introduce you to Microbiota data analysis and guide you through the analyses, visualization and interpretation of microbial community composition and diversity. This page contains important information on how to use this tutorial.

When working through the tutorial, you will encounter questions and exercises. Questions are intended to guide you through the analyses and help you identify some of the challenges of microbiota data analyses. Exercices are intended to aplly what you have learnt before. You can find answers by using the show/hide button of Solution section.

Before you begin, be sure you are all set up (see below).

Before you start

Before the training, please make sure you have done the following:

  1. Read the workshop Code of Conduct to make sure this workshop stays welcoming for everybody.
  2. Get comfortable: if you’re not in a physical workshop, be set up with two screens if possible. You will be following along in RStudio on your own computer while also following this tutorial on your own.
  3. Install R, RStudio and other packages following instructions in the Setup section.

Schedule

Setup Download files required for the lesson
00:00 1. Introduction What will I learn during this workshop?
00:30 2. Data preprocessing: from fastq to ASV How can I go from fasta files to ASV data?
02:00 3. Data exploration and properties Which packages do I need for the analyses?
How can I import my data in R?
What do the data sets look like?
What are the properties for the occurrence table?
03:30 4. Alpha-diversity What is alpha-diversity?
How can I calculate and plot alpha-diversity?
How can I test differences among treatments?
05:00 5. Data filtering and normalisation How can I filter and normalize my occurrence data?
05:30 6. Beta-diversity What is beta-diversity?
How can I calculate and plot beta-diversity?
How can I test differences among treatments?
06:30 7. Bacterial community composition How bacterial community composition is usually represented?
07:40 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.