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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
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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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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

Phylogenetic Analysis and Visualization

Phylogenetics is the study of the evolutionary relationships among species or other groups of organisms. It involves the use of molecular and computational techniques to construct phylogenetic trees, which depict the evolutionary history of the organisms under study.

In bioinformatics, phylogenetics is studied using various computational tools and methods, including sequence alignment, distance-based methods, maximum likelihood, and Bayesian inference. These methods allow researchers to compare DNA or protein sequences from different organisms and infer their evolutionary relationships based on similarities and differences in their genetic makeup. Phylogenetics has many applications in biology, and is used to help understand the evolutionary history of species, to study the origins and spread of diseases (phylogenetic analysis can be used to trace the origins and spread of infectious diseases), and to inform conservation efforts by identifying...

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