Chapter 2 Program
The course takes place on each working day from 9am – 1pm (CEST). Short breaks will be scheduled between sessions.
The hands-on sessions consists of a set of questions and example data. Solve the exercises by taking advantage of the online examples and resources that are pointed out in the study material. There is often more than one way to solve a given task. It is assumed that you have already installed the required software. Do not hesitate to ask support from the course assistants.
2.1 Monday 12 July: from raw sequences to ecological data analysis
Lectures
Microbiota analysis: association studies vs. causality; microbiota sequencing methods (16S, shotgun, metagenomics) - by dr. Tom Ederveen (Radboud UMC Nijmegen, The Netherlands)
DNA isolation and 16S rRNA gene sequencing; bioinformatics step 1: from raw sequences to OTU table in a biom file – by Tom Ederveen (Radboudumc Nijmegen, The Netherlands)
Demo & Practical
Importing data to R for interactive data analysis
Task: initialize reproducible report
2.2 Tuesday 13 July - Alpha diversity
Demo
- Microbiome data exploration
Lecture
- Key concepts in microbiome data science
Practical
- Alpha diversity: estimation, analysis, and visualization
2.3 Wednesday 14 July - Beta diversity
Demo
- Community similarity
Practical
- Beta diversity: estimation, analysis, and visualization
2.4 Thursday 15 July - Differential abundance
Lecture
- Differential abundance analysis methods
Practical
- Differential abundance in practice
Lecture
- Overview of microbiota data science methods & concepts
2.5 Friday 16 July: Presentations & closing
Student presentations on microbiome data analytics