Research talks:


Davis R Users’ Group (

  • Introduction to dplyr
    • Part 1 video (the stream got goofed, so the screen is frozen until min 28)
    • Part 1 code
    • Part 2 video
    • Part 2 code
  • Introduction to ggplot2

Meet and Analyze Data (

  • Introduction to automation with Snakemake: part 1
    • Description: Ever had some code stop running in the middle? Snakemake to the rescue! Need to switch from your local computer to the cloud? Snakemake can do that! Want a detailed, repeatable, automated description of everything you ran? Snakemake is your solution! Love conda? Snakemake.
    • Tutorial
    • Video
    • Data
  • Introduction to R Markdown
    • Description: This week we’ll learn about R Markdown and it’s many capabilities for weaving together narrative text and code to produce elegantly formatted outputs.
    • Video
  • Practical software management with conda, Pt 1
    • In bioinformatics, we often use mulitiple software tools to answer a research question. In this lesson, we will learn how to use conda environments to install and manage bioinformatics software. Conda will help us conduct reproducible analyses while avoiding software conflicts, and can save a lot of time and energy. Come experience the magic of conda!
    • Tutorial
    • Video
  • What is the shell?
    • Description: Most people use a mouse or trackpad to interact with our computer screens. However, this method is usually intractable for large data and bioinformatics. Instead, we use a computer operating system (Unix) to leverage a command-line interface (the shell). This makes repetitive tasks automatic and fast and helps wrangle extremely large datasets. We will give a brief introduction to working with the shell and some strategies for getting started. If you’re already familiar, feel free to come by and do your own work while picking up tips and tricks!
    • Tutorial
    • Video