R Bioinformatics Cookbook

Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem

Key Features

• Apply modern R packages to handle biological data using real-world examples
• Represent biological data with advanced visualizations suitable for research and publications
• Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses

Book Description

Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples.

This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse.

By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data.

What you will learn

• Employ Bioconductor to determine differential expressions in RNAseq data
• Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels
• Use ggplot to create and annotate a range of visualizations
• Query external databases with Ensembl to find functional genomics information
• Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics
• Use d3.js and Plotly to create dynamic and interactive web graphics
• Use k-nearest neighbors, support vector machines and random forests to find groups and classify data

Who this book is for

This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.

Table of Contents

1. Performing Quantitative RNAseq
2. Finding Genetic Variants With Next-Generation Sequence Data
3. Analyzing Gene and Protein Sequence For Domains and Motifs
4. Phylogenetic Analysis and Visualisation
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 in Bioinformatics
10. Programming and Analysis with Tidyverse
11. Building reusable workflows with packages and objects for code re-use

Professor Dan MacLean has a Ph.D. in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now a Honorary Professor in the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor and developing analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at The Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python with over 100,000 downloads combined.