About the Book
Part I Groundwork
1. Overview of Sequence Data Formats
Hongen Zhang
2. Integrative Exploratory Analysis of Two or More Genomic Datasets
Chen Meng and Aedin Culhane
3. Study Design for Sequencing Studies
Loren Honaas, Naomi Altman, and Martin Krzywinski
4. Genomic Annotation Resources in R/Bioconductor
Marc RJ Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, and Martin Morgan
Part II Public Genomic Data
5. The Gene Expression Omnibus Database
Emily Clough and Tanya Barrett
6. A Practical Guide to the Cancer Genome Atlas (TCGA)
Zhining Wang, Mark A. Jensen, and Jean Claude Zenklusen
Part III Applications
7. Working with Oligonucleotide Arrays
Benilton S. Carvalho
8. Meta-Analysis in Gene Expression Studies
Levi Waldron and Markus Riester
9. Practical Analysis of Genome Contact Interaction Experiments
Mark A. Carty and Olivier Elemento
10. Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data
Matthias Lienhard and Lukas Chavez
11. Variant Calling From Next Generation Sequence Data
Nancy F. Hansen
12. Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes
Songjoon Baek and Myong-Hee Sung Part IV Tools
13. NGS-QC Generator: A Quality Control System for ChIP-seq and Related Deep Sequencing-Generated Datasets
Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Matthias Blum, Pierre Etienne Cholley, and Hinrich Gronemeyer
14. Operating on Genomic Ranges Using BEDOPS
Shane Neph, Alex P. Reynolds, M. Scott Kuehn, and John A. Stamatoyannopoulos
15. GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality
Thomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker, and Matthew Brauer
16. Visualizing Genomic Data using Gviz and Bioconductor
Florian Hahne and Robert Ivanek
17. Introducing Machine Learning Concepts with WEKA
Tony C. Smith and Eibe Frank
18. Experimental Design and Power Calculation for RNA-Seq Experiments
Zhijin Wu and Hao Wu 19. It's DE-licious: A Recipe for Differential Expression Analyses of RNA-Seq Experiments Using Quasi-Likelihood Methods in EdgeR
Aaron T.L. Lun, Yunshun Chen, and Gordon K. Smyth
