Summary and Setup

This is lesson is for microbiome analysis using R/Bioconductor. This lesson shows through concrete examples how you can take advantage of the latest developments in R/Bioconductor for the manipulation, analysis, and reproducible reporting of hierarchical and heterogeneous microbiome profiling data sets.

Learning objectives

After attending this course, learners will be able to:

  • Importing microbiome data as TreeSummarizedExperiment object.
  • Estimate alpha diversity indices (Shannon, Faith’s, evenness and richness).
  • Estimate beta diversity by applying Principal Coordinate Analysis (PCoA).
  • Performing differential abundance analysis by utilizing Maaslin3.
Prerequisite
  • Basic understanding of microbiome concepts
  • Basic R programming
  • familiarity with data sctructures and tabular data in R
  • Basic understanding of statistics

FIXME: Setup instructions live in this document. Please specify the tools and the data sets the Learner needs to have installed.

Data Sets

Download the data zip file and unzip it to your Desktop

Software Setup

Discussion

Details

Setup for different systems can be presented in dropdown menus via a spoiler tag. They will join to this discussion block, so you can give a general overview of the software used in this lesson here and fill out the individual operating systems (and potentially add more, e.g. online setup) in the solutions blocks.

Use PuTTY

Use Terminal.app

Use Terminal