Get Ready

Exercises in R will be a central part of the workshop. Make sure a more recent version of R and RStudio is running on your computer. The following R packages are essential. There will be more libraries but this is a starting point. For installation support and ideas see R Help.

CRAN Packages

• ape - Analyses of Phylogenetics and Evolution
• DT - A Wrapper of the JavaScript Library DataTables
• gridExtra - Arrange Multiple Grid-Based Plots
• Hmisc - Harrell Miscellaneous
• igraph - Pain-Free Implementation of Graph Algorithms
• iml - Tools for Analysing Machine Learning Models
• pander - Rendering R Objects into Pandocs Markdown
• plotly - Advanced Scatter and Line Plots
• plyr - Splitting, Applying and Combining
• randomForest - Random Forests for Classification and Regression
• ranger - Fast Implementation of Random Forests
• sciplot - Scientific Graphing Functions for Factorial Designs
• Tidyverse - Collection of R Packages, including ggplot2, dplyr, etc.
• vegan - Community Ecology Package

Bioconductor Packages

• phyloseq - Analyze Microbiome Census Data
• microbiome - Utilities for Microbiome Analysis
• DESeq2 - Differential Gene Expression Analysis