R Bioinformatics Cookbook: Use R and Bioconductor to perform RNAseq,genomics,data visualization,and bioinformatic analysis
Authors: Dan MacLean
ISBN-10: 1789950694
ISBN-13: 9781789950694
Publisher finelybook 出版社: Packt Publishing (11 Oct. 2019)
Print Length 页数: 316 pages
Book Description
By finelybook
Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem
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
