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R Bioinformatics Cookbook

You're reading from   R Bioinformatics Cookbook Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis

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Product type Paperback
Published in Oct 2019
Publisher Packt
ISBN-13 9781789950694
Length 316 pages
Edition 1st Edition
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Authors (2):
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Dr Dan Maclean Dr Dan Maclean
Author Profile Icon Dr Dan Maclean
Dr Dan Maclean
Dan MacLean Dan MacLean
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Dan MacLean
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Toc

Table of Contents (13) Chapters Close

Preface 1. Performing Quantitative RNAseq 2. Finding Genetic Variants with HTS Data FREE CHAPTER 3. Searching Genes and Proteins for Domains and Motifs 4. Phylogenetic Analysis and Visualization 5. Metagenomics 6. Proteomics from Spectrum to Annotation 7. Producing Publication and Web-Ready Visualizations 8. Working with Databases and Remote Data Sources 9. Useful Statistical and Machine Learning Methods 10. Programming with Tidyverse and Bioconductor 11. Building Objects and Packages for Code Reuse 12. Other Books You May Enjoy

To get the most out of this book

Good knowledge of R and its various libraries is mandatory for this book.

Download the example code files

You can download the example code files for this book from your account at www.packt.com. If you purchased this book elsewhere, you can visit www.packtpub.com/support and register to have the files emailed directly to you.

You can download the code files by following these steps:

  1. Log in or register at www.packt.com.
  2. Select the Support tab.
  3. Click on Code Downloads.
  4. Enter the name of the book in the Search box and follow the onscreen instructions.

Once the file is downloaded, please make sure that you unzip or extract the folder using the latest version of:

  • WinRAR/7-Zip for Windows
  • Zipeg/iZip/UnRarX for Mac
  • 7-Zip/PeaZip for Linux

The code bundle for the book is also hosted on GitHub at https://github.com/PacktPublishing/R-Bioinformatics-Cookbook. In case there's an update to the code, it will be updated on the existing GitHub repository.

We also have other code bundles from our rich catalog of books and videos available at https://github.com/PacktPublishing/. Check them out!

Download the color images

Conventions usedpacktpub.com/.../9781789950694_ColorImages.pdf

There are a number of text conventions used throughout this book.

CodeInText: Indicates code words in text, database table names, folder names, filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles. Here is an example: "We'll look at using the ape and treeio packages to get tree data into and out of R. "

A block of code is set as follows:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()

Bold: Indicates a new term, an important word, or words that you see on screen. For example, words in menus or dialog boxes appear in the text like this. Here is an example: "Some of the dependencies rely on encapsulated Java code, so you'll need to install a Java Runtime Environment (JRE) for your system."

Warnings or important notes appear like this.
Tips and tricks appear like this.

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