Overview

The State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes. Balanced Coverage of Theory and Practice.Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software. The Tools and Methods to Get Started in Your Lab. Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed overview of the main RNA-seq data analysis methods and explains how to use them in practice. It is suitable for researchers from a wide variety of backgrounds, including biology, medicine, genetics, and computer science. The book can also be used in a graduate or advanced undergraduate course.

Full Product Details

Author:   Eija Korpelainen (CSC - IT Center for Science, Espoo, Finland) ,  Jarno Tuimala (RS-koulutus, Helsinki, Finland) ,  Panu Somervuo (University of Helsinki, Finland) ,  Mikael Huss (SciLifeLab, Stockholm University, Sweden)
Publisher:   Taylor & Francis Inc
Imprint:   CRC Press Inc
Dimensions:   Width: 15.60cm , Height: 2.00cm , Length: 23.40cm
Weight:   0.640kg
ISBN:  

9781466595002

ISBN 10:   1466595000
Pages:   324
Publication Date:   19 September 2014
Audience:   Professional and scholarly ,  Professional and scholarly ,  Professional & Vocational ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   In Print  
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Table of Contents

Reviews

RNA-seq is currently the best method for genome-wide transcriptional profiling of cells in about any organism. This book includes all the key steps, in generally the same organization, that we've found to be effective when training biologists and bioinformaticians in RNA-seq analysis. It's a good guide and reference for RNA-seq that can get analysts started (or keep them going) while avoiding much of the time-consuming literature, documentation, and Web searches at each step of the pipeline. It covers a broad (but not overwhelming) selection of popular methods without the typical bias of an author's research emphasis. -George W. Bell, Ph.D., Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA In modern life sciences, it is increasingly the bioinformatics aspect that holds the essential key to successful research projects and discoveries, albeit often poorly understood, or even regarded as a 'black box.' This is precisely the point at which RNA-seq Data Analysis: A Practical Approach comes in. This book, a brilliant compilation of all different aspects of RNA-sequencing analyses, opens up this 'black box' and reveals all of its inner workings. It covers all the basic principles while maintaining a tight focus on the practical aspects of successful analyses, including discussing caveats and possible pitfalls. Following this spirit throughout, it is intuitively structured and easy to read, making it attractive both for researchers who want to quickly deepen their understanding of RNA-seq processing and for use as teaching material in the classroom for the scientists of the future. -Manfred Grabherr, Department of Medical Biochemistry and Microbiology, Uppsala University I feel that this is a marvelous book and will be of invaluable use to support bioinformaticians, graduate students, and the occasional user of the RNA-seq technology. It has great depth of content and addresses the key areas of designing your study and making sense of the data. It covers the typical scenarios that a services bioinformatician is likely to encounter and I can see this book having a place on desks of scientists across academia and industry. -Stephen Rudd, Head of Computational Biology, University of Queensland I strongly recommend RNA-seq Data Analysis: A Practical Approach to any scientist who plans to do sequencing experiments, even if he will not analyze the data by himself. The book gives in the first parts very important outlines of the sequencing technology and how it is working. ... Going further, the book covers all state-of-the-art techniques of RNA-seq analysis in a very profound yet clear way and will be of great value even for the advanced bioinformatician as a reference work. ... a must-have recommendation to everyone working in the molecular biology field ... Even as a bioinformatician with over 15 years of experience in this field, I found many valuable details and some yet not known facts about sequencing data analysis. -Oliver Heil, Bioinformatician, German Cancer Research Center (DKFZ) Many people are interested in applying RNA-seq to examine the transcriptome of their organism of interest but they are finding it difficult to apply it in their own laboratories. ... In this book, RNA-seq is introduced by describing the different platforms and then the reader is taken in a systematic way through the process of analyzing RNA-seq data using several free open source tools. This book will be of interest to people starting with RNA-seq. -Dr. Etienne de Villiers, Bioinformatics Group Leader, KEMRI-Wellcome Trust Research Programme (KWTRP), and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford

I strongly recommend RNA-seq Data Analysis: A Practical Approach to any scientist who plans to do sequencing experiments, even if he will not analyze the data by himself. The book gives in the first parts very important outlines of the sequencing technology and how it is working. ... Going further, the book covers all state-of-the-art techniques of RNA-seq analysis in a very profound yet clear way and will be of great value even for the advanced bioinformatician as a reference work. ... a must-have recommendation to everyone working in the molecular biology field ... Even as a bioinformatician with over 15 years of experience in this field, I found many valuable details and some yet not known facts about sequencing data analysis. -Oliver Heil, Bioinformatician, German Cancer Research Center (DKFZ) Many people are interested in applying RNA-seq to examine the transcriptome of their organism of interest but they are finding it difficult to apply it in their own laboratories. ... In this book, RNA-seq is introduced by describing the different platforms and then the reader is taken in a systematic way through the process of analyzing RNA-seq data using several free open source tools. This book will be of interest to people starting with RNA-seq. -Dr. Etienne de Villiers, Bioinformatics Group Leader, KEMRI-Wellcome Trust Research Programme (KWTRP), and Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford

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Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, Garry Wong

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