Precourse

These are absolutely necessary for the course, if you do not already have a working R environment with R studio:

Download and install the latest version of R from r-project.org. Install Rtools from https://cran.r-project.org/bin/. Rtools may be needed for installing new packages from source.

Install RStudio. RStudio provides you with tools like code editor with highlighting, project management, version control, package building, debugger, profiler and more.

install R packages necessary for this course:

install.packages(c("ggplot2","tidyverse","ggmap","pheatmap","devtools","cowplot",
                   "reshape2", "dplyr", "wesanderson", "scales", "ggthemes", "ggrepel",
                   "ggpubr", "gridExtra", "gganimate", "shiny", "rsconnect",
                   "grid", "shinythemes", "colourpicker"), dependencies = TRUE)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("ggtree", "treeio"))

To make sure that the installations went well, we will try to make a quick plot using the packages you just installed. In this plot, we try to see if there is correlation plot between BMI and average no.of steps taken by some volunteers per day. The data and the code for plotting is available here. Just knit the Rmarkdown file and you should see correlation the plot, if all the packages are installed properly.

The following are the steps that are recommended for the course participants.

Although you would have a small session on how to handle data in R, it is advisable for you to freshen up your memory on data-types such as data.frame, matrix and read/write files and so on.
Some warm-up exercises in R if you are interested can be found here
The data that is necessary for this course is available here and it is important to check that the file-tree looks OK.

Precourse

HackMD