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R Bioinformatics Cookbook - Second Edition

You're reading from R Bioinformatics Cookbook - Second Edition

Product type Book

Published in Oct 2023

Publisher Packt

ISBN-13 9781837634279

Pages 396 pages

Edition 2nd Edition

Languages

Concepts

Author (1):

Dan MacLean

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

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

Using bioconda to install external tools

Using environments for packages in R is extremely useful for managing different versions for different projects. Bioinformatics pipelines often have numerous dependencies outside of R, including binary command-line programs and packages from other languages, and it can often be useful to put those under the same sort of management. Tools for that do exist.

Anaconda is a distribution of Python and R that is particularly popular for scientific computing, data science, and machine learning. It includes a large number of pre-installed packages and tools, such as NumPy, SciPy, and Jupyter, making it easy to get started with those technologies. Anaconda also includes the conda package manager, which can be used to install additional packages and manage environments. Bioconda is a distribution of bioinformatics software built on top of conda. It includes a wide variety of bioinformatics tools and libraries, making it easy to install and manage those...

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Authors (1)

Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.

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