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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
Author Profile Icon Dan MacLean
Dan MacLean
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Toc

Table of Contents (13) Chapters Close

Preface 1. Performing Quantitative RNAseq FREE CHAPTER 2. Finding Genetic Variants with HTS Data 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

Working with Databases and Remote Data Sources

Large-scale model organism sequencing projects, such as the Human Genome Project (HGP), or the 1,001 plant genomes sequencing projects have made a huge amount of genomics data publicly available. Likewise, open access data sharing by individual laboratories has made the raw sequencing data of genomes and transcriptomes widely available, too. Working with this data programmatically can mean having to parse or bring locally some seriously large or complicated files. As such, much effort has gone into making these resources as accessible as possible through APIs and other queryable interfaces, such as BioMart. In this chapter, we'll look at some recipes that will allow us to search for annotations without having to download whole genome files and find relevant information across databases. We'll look at how to pull raw reads...

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