Welcome to your introductory guide to computational research!
This guide has been created to walk you through basic software downloads and installations as well as highlighted chapters of the "R for Data Science" book.
This guide was created by Kaylee M. Delgado through the Vaske Lab at UC Santa Cruz; all software links reflect current version as of Q2 2024.
Read more about our research here: Treehouse Childhood Cancer Initiative
In order for science to be valid, it has to be reproducible. Luckily, this can be easier for computational biology experiments than in wet lab experiments. This training introduces you to a framework for making sure your future research is reproducible.
Throughout this training we will be working on the following:
- Using GitHub, RStudio, renv, and Quarto notebooks
- Building repositories, files, and pipelines
- Getting a hang of research computing workflows
- Learning computational research skills in R including: data visualization, data transformation, and program iteration.
Before you can work on a Treehouse computational project, you must demonstrate that you know how to perform reproducible experiments.
When you have completed this work described in this repo, your mentor will confirm that you have done the following, and you can proceed with research.
- Created a repository under the GitHub UCSC-Treehouse organization level
- Created a quarto notebook, branch and pull request for every chapter
- Run all the code examples, each in a separate chunk in the chapter's quarto notebook
- Done all the exercises, documenting your work and writing out your answers to questions like "How is this plot different?" in the chapter's quarto notebook
If you are not a Treehouse computational researcher, there will be two differences:
- You will store your repository in your own GitHub account, and
- You can review your own pull requests or request review from someone you know with relevant knowledge.
Go to Chapter_00_Instructions.
As you may quickly notice, there are two files for each chapter: .qmd and .md
For readability, you will likely want to follow along with the .md version.