Book Image

R Bioinformatics Cookbook

By : Dan MacLean
Book Image

R Bioinformatics Cookbook

By: Dan MacLean

Overview of this book

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.
Table of Contents (13 chapters)

Performing multiple alignments of genes or proteins

The alignment of sequences as a task prior to building phylogenetic trees or as an end in itself to determine conserved and divergent regions is a mainstay in bioinformatics analysis and is amply covered in R and Bioconductor with the ape and DECIPHER packages. We'll look at the extremely straightforward procedures for going from sequence to alignment in this recipe.

Note that there are different techniques for different sequence lengths. In this first recipe, we'll look at how to align some Kbp-length sequences such as those that represent genes and proteins.

Getting ready

This recipe needs the msa package. This is a pretty hefty package and includes external...