Packages

ggplot2: For plotting data ggplot2 is very useful - can be installed from CRAN

tidyverse: A collection of general data handling tools gaining much popularity within the R user community

phyloseq: There are several packages for handling microbiome type data. For this course we use phyloseq see tutorial

metagMisc: A package with functionallity for cross-talk between different packages found on github

vegan: Vegan is a very useful package with a lot of functionality. However, here we use only the adonis() function.

ape: For handling phylogenetic trees this package is good.

picante: Phylogenetic integration in analysis

DAtest: This a custome made single purpose package to be found on github

DESeq2: This package is developed for Differential Expression statistics for RNA-seq data. However, it is widely used for microbiome data as well.

metagenomeSeq: Is a package for handling microbiome data. Here, especially the differential abundance testing procedure featureModel() is used.

limma: A general package for multiple Differential Expression stats developed for RNA-seq.

variancePartition and edgeR: As limma, but makign mixed models doable, for instance from longitudinal / repeated measures experiments.

BiocParallel: Getting stuff to run quicker.

ggtree: A nice vizualisation package for plotting tree, build on top of ggplot2 functionality.

For details on installation and getting-started, please check vignettes, help-documentation, google, youtube,…. Most things are pretty easy to copy-paste and run from examples and then exchange with your own data.