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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

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:

  1. Install renv:
    install.packages("renv")
  2. Create a new renv environment:
    renv::init()

    This will create a new directory called .renv in your current project directory.

  3. You can then install packages with this:
    renv::install_packages()
  4. You can also use the renv package manager to install Bioconductor packages by running the following command:
    renv::install("bioc::package name")
  5. For example, to install the Biobase package, you would run the following:
    renv::install("bioc::Biobase")
  6. You can use renv to install development packages from GitHub like this:
    renv::install("user name/repo name")
  7. For example, to install the danmaclean user rbioinfcookbook package, you would run the following:
    renv::install...
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