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Statistical Genomics

Methods and Protocols

  • Ewy Mathé
  • Sean Davis

Part of the Methods in Molecular Biology book series (MIMB, volume 1418)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Groundwork

    1. Front Matter
      Pages 1-1
    2. Hongen Zhang
      Pages 3-17
    3. Loren A. Honaas, Naomi S. Altman, Martin Krzywinski
      Pages 39-66
    4. Marc R. J. Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, Martin Morgan
      Pages 67-90
  3. Public Genomic Data

    1. Front Matter
      Pages 91-91
    2. Emily Clough, Tanya Barrett
      Pages 93-110
    3. Zhining Wang, Mark A. Jensen, Jean Claude Zenklusen
      Pages 111-141
  4. Applications

    1. Front Matter
      Pages 143-143
    2. Benilton S. Carvalho
      Pages 145-159
    3. Levi Waldron, Markus Riester
      Pages 161-176
    4. Mark A. Carty, Olivier Elemento
      Pages 177-189
    5. Matthias Lienhard, Lukas Chavez
      Pages 191-208
  5. Tools

    1. Front Matter
      Pages 241-241
    2. Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Matthias Blum, Pierre-Etienne Cholley, Hinrich Gronemeyer
      Pages 243-265
    3. Shane Neph, Alex P. Reynolds, M. Scott Kuehn, John A. Stamatoyannopoulos
      Pages 267-281
    4. Thomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker, Matthew J. Brauer
      Pages 283-334
    5. Florian Hahne, Robert Ivanek
      Pages 335-351
    6. Tony C. Smith, Eibe Frank
      Pages 353-378
  6. Back Matter
    Pages 417-418

About this book

Introduction

This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls.

Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data.

Keywords

sequence data formats omnibus database oligonucleotide arrays gene expression studies genome contact interaction experiments genome-scale analysis bioconductor RNA-seq experiments

Editors and affiliations

  • Ewy Mathé
    • 1
  • Sean Davis
    • 2
  1. 1.Ohio State UniversityBiomed Informatics, College of MedicineColumbusUSA
  2. 2.National Cancer InstituteNational Institutes of HealthColumbiaUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-4939-3578-9
  • Copyright Information Springer Science+Business Media New York 2016
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-3576-5
  • Online ISBN 978-1-4939-3578-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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