Working with biological data with R

Workshop webpage and resources

Workshop links (this page) - https://anatmela.github.io/20250407-RWorkshop
Carpentries code of conduct

Workshop (Anonymous) survey - please fill

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Workshop structure and links

Session 1

Data entry and storage

• ‘messy’ and ‘tidy’ data
• Data entry using excel
• File formats

Introduction to R and Rstudio

• why R
• The R studio environment
• Project management
• Seeking help
• Read in data file, writing data to file

Session 2

Working with data in R

• Data structures
• Exploring data frames
• Subsetting data
  • Take home assignment

Session 3

Creating Publication-Quality Graphics with ggplot2

• Control flow
• data types
• ggplot2
  • Take home assignment

Session 4

Producing reports with knitr and markdown

• Introduction to the tidyverse
• Producing Reports With knitr and rmarkdown
  • Assignment in class
    
    

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Optional further reading and resources

• The Carpentries

• Data carpentry for Biologist - additional course materials

• R for Reproducible Scientific Analysis - additional course materials

• R for data science (eBook)

• R Markdown: the definitive guide (eBook)

• Posit cheet sheets (Also in Rstudio: Help -> Cheat Sheets)

• Good enough practices in scientific computing

• A Quick Guide to Organizing Computational Biology Projects

• Ten simple rules for biologists learning to program

• Ten Simple Rules for Reproducible Computational Research