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R Bioinformatics Cookbook

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

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Product type Paperback
Published in Oct 2023
Publisher Packt
ISBN-13 9781837634279
Length 396 pages
Edition 2nd Edition
Languages
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Author (1):
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Dan MacLean Dan MacLean
Author Profile Icon Dan MacLean
Dan MacLean
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Toc

Table of Contents (16) Chapters Close

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 15. Other Books You May Enjoy

To get the most out of this book

The book assumes that you have a basic working knowledge of R in the console and that you have a background in biology or life sciences. The book won’t try and teach you any biology; instead, we concentrate on applications of R within science. You will learn lots of new things about R that will enhance your bioinformatics research.

Software/hardware covered in the book

Operating system requirements

R 4.2 or greater

Windows, macOS, or Linux

Python 3.8 or greater

Windows, macOS, or Linux

Many individual R packages and some external tools are needed. All these will be discussed in the relevant chapters and recipes so make sure to read the Getting ready… sections.

If you are using the digital version of this book, we advise you to type the code yourself or access the code from the book’s GitHub repository (a link is available in the next section). Doing so will help you avoid any potential errors related to the copying and pasting of code.

The sample data for this book is provided in an R package that you can install from within R. Look out for advice on how to do that in the relevant chapters and recipes. The code won’t work without the sample data, so look out for that.

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