You're reading from R Bioinformatics Cookbook Utilize R packages for bioinformatics, genomics, data science, and machine learning

Product type Paperback

Published in Oct 2023

Publisher Packt

ISBN-13 9781837634279

Length 396 pages

Edition 2nd Edition

Languages

Tools

ChatGPT

Concepts

Bioinformatics

Author (1):

MacLean

View More author details

Table of Contents (16) Chapters

Preface

1. Chapter 1: Setting Up Your R Bioinformatics Working Environment

2. Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse FREE CHAPTER

3. Chapter 3: ggplot2 and Extensions for Publication Quality Plots

4. Chapter 4: Using Quarto to Make Data-Rich Reports, Presentations, and Websites

5. Chapter 5: Easily Performing Statistical Tests Using Linear Models

6. Chapter 6: Performing Quantitative RNA-seq

7. Chapter 7: Finding Genetic Variants with HTS Data

8. Chapter 8: Searching Gene and Protein Sequences for Domains and Motifs

9. Chapter 9: Phylogenetic Analysis and Visualization

10. Chapter 10: Analyzing Gene Annotations

11. Chapter 11: Machine Learning with mlr3

12. Chapter 12: Functional Programming with purrr and base R

13. Chapter 13: Turbo-Charging Development in R with ChatGPT

14. Index

Why subscribe?

15. Other Books You May Enjoy

Technical requirements

We will use renv to manage packages in a project-specific way. To use renv to install packages, you will first need to install the renv package. You can do this by running the following commands in your R console:

Install renv:
```
install.packages("renv")
```
Create a new renv environment:
```
renv::init()
```
This will create a new directory called .renv in your current project directory.
You can then install packages with the following:
```
renv::install_packages()
```

For this chapter, we’ll need the following packages:

Regular packages:
- ggplot2
- tidyr

Further information

Not all the recipes in this section happen in R; in fact, most happen in the chat window of ChatGPT. Make an account for this at https://chat.openai.com/. I’ll include results from ChatGPT inline in the recipe steps.