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.

Slides

Topics

Setup

This workshop is designed to work with RStudio Cloud. Go to https://rstudio.cloud/ (Monash users can log in with their Monash google account) and create a new project.

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("devtools")
install.packages("usethis")
install.packages("BiocManager")
BiocManager::install("edgeR")

Files

The workshop files downloaded by the setup instructions above are also available here:

See also

In this series:

Other resources:


Authors

This course was developed by Paul Harrison and Richard Beare for Monash Data Fluency and the Monash Bioinformatics Platform.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Source code