GCC AMR Using R to Analyze and Display Microbiome Data Workshop

Agenda

9:30-9:45 | Introduction and Setup

Topics:

- Brief overview of microbiome data structures

- Loading data into R

- Data pre-processing

- Review of key packages

9:45-10:15 | Describing the Microbiome - Alpha Diversity

Topics:

- Summarizing composition by taxonomy level

- Alpha diversity metrics

- Visualizing community composition

10:15-10:55 | Comparing Samples - Beta Diversity and Ordination

Topics:

- Distance Metrics

- Ordination Methods

- Adding metadata and estimating confidence

10:55-11:05 | Break

11:05-11:40 | Co-Occurrence and Network Visualizations

Topics:

- Detecting and visualizing microbiome associations

- Correlation methods

- Graph-based visualization

11:40-12:10 | Linking microbiome to metadata

Topics:

- Constrained ordination

- Correlation heatmaps

12:10-12:30 | Wrap-up and discussion