These are the course notes for the Monash Data Fluency’s “Programming and Tidy data analysis in R” course. This is an intermediate level R workshop, for people wishing to increase their fluency in R. It covers tasks that while not specifically involved in statistical analysis are necessary when working with data: loading data and getting it into a form that is easy to work with, automating repetitive tasks, identifying problems such as the need for normalization and transformation, and properly understanding the story the data wants to tell.
Running the R code below will download files and install packages used in this workshop. This should also work for R used locally, excepting that to use FastQC you will need to have installed Java, and the FastQC steps will probably need some adjustments for Windows computers (this isn’t an essential part of the workshop).
# Download workshop files download.file( "https://monashdatafluency.github.io/r-progtidy/r-progtidy-files.zip", "r-progtidy-files.zip") unzip("r-progtidy-files.zip") # Download FastQC software download.file( "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip", "fastqc_v0.11.8.zip") unzip("fastqc_v0.11.8.zip") system("chmod u+x FastQC/fastqc") # Install Tidyverse packages install.packages("tidyverse") # Optional: install some further packages # (these are mentioned but not essential to the workshop) install.packages("rmarkdown") install.packages("devtools") install.packages("usethis") install.packages("BiocManager") BiocManager::install("edgeR")
The workshop files downloaded by the setup instructions above are also available here:
In this series: