QuantBio2019 workshop in Fiesch

Presentation, the code, and exercises to accompany the QuantBio workshop in Fiesch, 15-20 September, 2019.

File description

• presentation-intro.pdf introductory presentation with background information.
• presentation-main.Rpres and html R presentation with workshop lecture and exercises.
• analysis-student.Rmd R notebook with the analysis for exercises. Contains the code with placeholders to fill in during the workshop. Can be compiled (in Rstudio) to a final html document.
• analysis-main.Rmd and html. R notebook with full analysis from raw data to plots. The associated html file contains a final document with code and results.
• data folder with raw in intermediate data files.

Required packages

The workflow is written in R and takes advantage of RStudio notebooks. Please download the latest RStudio from here.

The analysis uses the following packages that need to be present in your RStudio installation:

• data.table for fast processing of large datasets
• readxl for reading Excel files
• R.utils for directly reading comressed files
• imputeTS for data imputation such as interpolation of NA's
• ggplot2 for plotting
• plotly for interactive plots
• gplots for plotting heatmaps
• d3heatmap for plotting interactive heatmaps
• dendextend for modifying dendrograms
• RColorBrewer for extended colour palettes
• scales for percentages on y-axis in ggplots
• dtwclust for dynamic time warping distance measure
• magrittr for pipes (typically loaded by other packages)
• factoextra for extracting and visualisation of the results of multivariate data analyses
• cluster for extended cluster analysis
• NbClust for determining the best number of clusters

Install these packages by typing:

install.packages(c(
					"data.table", "tidyverse",
					"readxl", "R.utils",
					"ggplot2", "gplots", "plotly", "d3heatmap",
					"dendextend", "RColorBrewer", "scales",
					"imputeTS", 
					"dtwclust", "factoextra", "cluster", "NbClust"))