Introduction to Bioinformatics with R: A Practical Guide for Biologists, 1st Edition (Paperback) book cover

Introduction to Bioinformatics with R

A Practical Guide for Biologists, 1st Edition

By Edward Curry

Chapman and Hall/CRC

296 pages | 75 Color Illus.

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Description

In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions.

Key Features:

· Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming.

· Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles

· Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves.

· Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens.

· Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research.

This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills.

Table of Contents

Introduction

Introduction to R

An Introduction to LINUX for Biological Research

Statistical Methods for Data Analysis

Analyzing Generic Tabular Numeric Datasets in R

Functional Enrichment Analysis

Integrating Multiple Datasets in R

Analyzing Microarray Data in R

Analyzing DNA Methylation Microarray Data in R

DNA Analysis With Microarrays

Working with Sequencing Data

Genomic Sequence Profiling

ChIP-seq

RNA-seq

Bisulphite Sequencing

Final Notes

About the Author

Ed Curry is a research fellow at Imperial College London, where he teaches topics in bioinformatics to biomedical scientists and
clinicians at both undergraduate and postgraduate level. He established a successful continuing professional development course
‘Introduction to Bioinformatics for Cancer Research’ which ran from 2012-2015. From 2015 his short course has run as part of the
bioinformatics teaching for the ‘Cancer Informatics’ masters programme, for which he is senior tutor.

About the Series

Chapman & Hall/CRC Computational Biology Series

This series aims to capture new developments in computational biology, as well as high-quality work summarizing or contributing to more established topics. Publishing a broad range of reference works, textbooks, and handbooks, the series is designed to appeal to students, researchers, and professionals in all areas of computational biology, including genomics, proteomics, and cancer computational biology, as well as interdisciplinary researchers involved in associated fields, such as bioinformatics and systems biology.

For more information or to submit a book proposal, please contact <a href="[email protected]">Elliott Morsia</a> ([email protected]).

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI008000
SCIENCE / Life Sciences / Biology / General
SCI010000
SCIENCE / Biotechnology