Abstract is missing.
- Overview of Sequence Data FormatsHongen Zhang. 3-17 [doi]
- Integrative Exploratory Analysis of Two or More Genomic DatasetsChen Meng, Aedín C. Culhane. 19-38 [doi]
- Study Design for Sequencing StudiesLoren A. Honaas, Naomi S. Altman, Martin Krzywinski. 39-66 [doi]
- Genomic Annotation Resources in R/BioconductorMarc Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, Martin Morgan. 67-90 [doi]
- The Gene Expression Omnibus DatabaseEmily Clough, Tanya Barrett. 93-110 [doi]
- A Practical Guide to The Cancer Genome Atlas (TCGA)Zhining Wang, Mark A. Jensen, Jean-Claude Zenklusen. 111-141 [doi]
- Working with Oligonucleotide ArraysBenilton S. Carvalho. 145-159 [doi]
- Meta-Analysis in Gene Expression StudiesLevi Waldron, Markus Riester. 161-176 [doi]
- Practical Analysis of Genome Contact Interaction ExperimentsMark A. Carty, Olivier Elemento. 177-189 [doi]
- Quantitative Comparison of Large-Scale DNA Enrichment Sequencing DataMatthias Lienhard, Lukas Chavez. 191-208 [doi]
- Variant Calling From Next Generation Sequence DataNancy F. Hansen. 209-224 [doi]
- Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear EnzymesSongjoon Baek, Myong-Hee Sung. 225-240 [doi]
- NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated DatasetsMarco-Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Matthias Blum, Pierre-Etienne Cholley, Hinrich Gronemeyer. 243-265 [doi]
- Operating on Genomic Ranges Using BEDOPSShane J. Neph, Alex P. Reynolds, Scott Kuehn, John A. Stamatoyannopoulos. 267-281 [doi]
- GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and FunctionalityThomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker, Matthew J. Brauer. 283-334 [doi]
- Visualizing Genomic Data Using Gviz and BioconductorFlorian Hahne, Robert Ivanek. 335-351 [doi]
- Introducing Machine Learning Concepts with WEKATony C. Smith, Eibe Frank. 353-378 [doi]
- Experimental Design and Power Calculation for RNA-seq ExperimentsZhijin Wu, Hao Wu 0003. 379-390 [doi]
- It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeRAaron T. L. Lun, Yunshun Chen, Gordon K. Smyth. 391-416 [doi]