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R Bioinformatics Cookbook - Second Edition

You're reading from R Bioinformatics Cookbook - Second Edition

Product type Book

Published in Oct 2023

Publisher Packt

ISBN-13 9781837634279

Pages 396 pages

Edition 2nd Edition

Languages

Concepts

Author (1):

Dan MacLean

Table of Contents (16) Chapters

Preface

1. Chapter 1: Setting Up Your R Bioinformatics Working Environment

2. Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse

3. Chapter 3: ggplot2 and Extensions for Publication Quality Plots

4. Chapter 4: Using Quarto to Make Data-Rich Reports, Presentations, and Websites

5. Chapter 5: Easily Performing Statistical Tests Using Linear Models

6. Chapter 6: Performing Quantitative RNA-seq

7. Chapter 7: Finding Genetic Variants with HTS Data

8. Chapter 8: Searching Gene and Protein Sequences for Domains and Motifs

9. Chapter 9: Phylogenetic Analysis and Visualization

10. Chapter 10: Analyzing Gene Annotations

11. Chapter 11: Machine Learning with mlr3

12. Chapter 12: Functional Programming with purrr and base R

13. Chapter 13: Turbo-Charging Development in R with ChatGPT

14. Index

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15. Other Books You May Enjoy

Finding allele-specific expression with AllelicImbalance

Allele-specific expression (ASE) refers to the differential expression of alleles (different versions of a gene) in a diploid organism. It occurs when one allele is expressed more or less than the other allele, resulting in an imbalance of expression. ASE can occur in both coding and non-coding regions of the genome and can have a significant impact on the phenotype of an organism. Analyzing ASE can help with identifying genetic variations that contribute to the development of diseases such as cancer and inherited disorders.

The R Bioconductor AllelicImbalance package can be used to analyze ASE data. This package provides a set of tools for identifying, quantifying, and visualizing ASE in high-throughput sequencing data. The package can be used to quantify ASE at both the gene and transcript level and to identify differentially expressed alleles. Additionally, AllelicImbalance can help identify the genomic regions that are...

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Authors (1)

Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at 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 has developed 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.

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