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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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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

Creating websites from collections of Quarto documents

Pandoc is a versatile tool that can convert documents between many different formats, including Markdown, HTML, LaTeX, and PDF. It can be used to convert a collection of Markdown documents into a static website. The basic workflow is to write the content in Markdown files, use Pandoc to convert the Markdown files to HTML files, and then serve the HTML files using a web server. Quarto enables this workflow by providing style templates, a series of extra markup, and rendering configurations that simplify the render through Pandoc.

The produced website can be hosted like any other. Of particular, but perhaps not obvious, utility for bioinformaticians is GitHub, which can be used as a hosting platform for the static website. GitHub allows users to create a repository to store the rendered sites, and then use GitHub Pages to host the static website. GitHub Pages is a free service that can host static websites that are built from...

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