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Bioconductor Case Studies

  • Florian Hahne
  • Wolfgang Huber
  • Robert Gentleman
  • Seth Falcon

Part of the Use R! book series (USE R)

Table of contents

  1. Front Matter
    Pages I-XI
  2. F. Hahne, R. Gentleman
    Pages 1-4
  3. R. Gentleman, F. Hahne, S. Falcon, M. Morgan
    Pages 5-24
  4. R. Gentleman, W. Huber
    Pages 25-45
  5. Florian Hahne, Wolfgang Huber
    Pages 47-61
  6. F. Hahne, W. Huber
    Pages 83-88
  7. W. Huber, D. Scholtens, F. Hahne, A. von Heydebreck
    Pages 89-102
  8. W. Huber, F. Hahne
    Pages 103-119
  9. R. Gentleman, W. Huber, V. J. Carey
    Pages 121-136
  10. R. Gentleman, V. J. Carey
    Pages 137-157
  11. T. Chiang, S. Falcon, F. Hahne, W. Huber
    Pages 159-172
  12. F. Hahne, W. Huber, R. Gentleman
    Pages 173-191
  13. R. Gentleman, M. Morgan, W. Huber
    Pages 193-205
  14. S. Falcon, R. Gentleman
    Pages 207-220
  15. Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon
    Pages 221-269
  16. Back Matter
    Pages 271-283

About this book

Introduction

Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include

* import and preprocessing of data from various sources

* statistical modeling of differential gene expression

* biological metadata

* application of graphs and graph rendering

* machine learning for clustering and classification problems

* gene set enrichment analysis

Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.

The authors of this book have longtime experience in teaching introductory and advanced courses to the application of Bioconductor software. Florian Hahne is a Postdoc at the Fred Hutchinson Cancer Research Center in Seattle, developing novel methodologies for the analysis of high-throughput cell-biological data. Wolfgang Huber is a research group leader in the European Molecular Biology Laboratory at the European Bioinformatics Institute in Cambridge. He has wide-ranging experience in the development of methods for the analysis of functional genomics experiments. Robert Gentleman is Head of the Program in Computational Biology at the Fred Hutchinson Cancer Research Center in Seattle, and he is one of the two authors of the original R system. Seth Falcon is a member of the R core team and former project manager and developer for the Bioconductor project.

Keywords

Annotation Bioinformatics Clustering Computational biology Computer Machine learning Microarray Networks biology calculus classification genome modeling

Authors and affiliations

  • Florian Hahne
    • 1
  • Wolfgang Huber
    • 2
  • Robert Gentleman
    • 3
  • Seth Falcon
    • 4
  1. 1.Division of Public Health Sciences, Program in Computational BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Wellcome Trust Genome CampusEuropean Bioinformatics Institute, EMBL Outstation HinxtonCambridgeUK
  3. 3.Division of Public Health Sciences, Program in Computational BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  4. 4.Scientific Software EngineerSeattleUSA

Bibliographic information