Install R, and Rstudio
These can be installed directly using install.packages()
ggplot2: For plotting data ggplot2 is very useful - can be installed from CRAN
ggpubr: For modifying ggplot2 plots to be even more informative
ggrepel, ggnetwork and pheatmap: additional plotting tools
tidyverse: A collection of general data handling tools gaining much popularity within the R user community
broom: A tidyverse add-on making it easy to compute the same type of model across subsets of data and/or several response variables
picante: Phylogenetic integration in analysis
ape: For handling phylogenetic trees this package is good.
vegan: Vegan is a very useful package with a lot of functionality. However, here we use only the adonis() function.
phyloseqGraphTest and compositions: Specific tools microbiome data
mediation: For mediating / triangulating effects
caret: General machine learning in R
readr, glue, reshape2, DT, lsmeans, and devtools: additional tools for making life easier.
BiocManager: A package to install things from Bioconductor
These can be installed using the BiocManager package: BiocManager::install()
phyloseq: There are several packages for handling microbiome type data. For this course we use phyloseq see tutorial
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.
ggtree: A nice vizualisation package for plotting tree, build on top of ggplot2 functionality.
BiocParallel: Getting stuff to run quicker.
vsn: Normalizing toolbox ported from Microarray data analysis.
These can be installed using the packages devtools or remotes (both available on CRAN) usign devtools::install_github() or remotes::install_github()
metagMisc: A package with functionallity for cross-talk between different packages found on github
DAtest: This a custome made single purpose package to be found on github
qiime2R: Package for porting between QIIME (python environment) and R. Can be installed by devtools::install_github(“jbisanz/qiime2R”).
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.