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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

Creating a tSNE and UMAP embedding

t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP) are both dimensionality reduction techniques commonly used in ML and data visualization.

t-SNE is a non-linear technique that aims to visualize high-dimensional data in a lower-dimensional space while preserving the local structure of the data. t-SNE is particularly useful for revealing clusters or groups of data points that may not be immediately apparent in the original high-dimensional space.

UMAP is another non-linear dimensionality reduction technique that has gained popularity due to its scalability and efficiency. UMAP also focuses on preserving local structures and employs a different mathematical method based on graph theory and optimization techniques. UMAP is often used for visualizing large datasets with millions of data points.

Both algorithms suffer from being computationally expensive, especially when dealing with large...

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