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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

Technical requirements

You will need to install Quarto, which can be done by selecting the relevant package for your operating system at this link: https://quarto.org/docs/get-started/.

  1. Quarto has a dependency on LaTeX, but once Quarto is installed, it can install a version of that for you. To install that, use the following command:
    quarto install tool tinytex

    From the command line, after you’ve installed Quarto, all should be ready.

    To render, we’ll use the command-line options, and I’ll make this explicit in each recipe. If you want to take advantage of Quarto’s integration into RStudio, you’ll need to make sure that you have installed RStudio version 2022.07 or later, which has support in the integrated development environment (IDE) for Quarto. Install that from here: https://rstudio.com/products/rstudio/download/.

  2. We will use renv to manage packages in a project-specific way. To use renv to install packages, you will first need to install...
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