Statistical Genomics

Overview of Sequence Data Formats.- Integrative Exploratory Analysis of Two or More Genomic Datasets.- Study Design for Sequencing Studies.- Genomic Annotation Resources in R/Bioconductor.- The Gene Expression Omnibus Database.- A Practical Guide to the Cancer Genome Atlas (TCGA).- Working with Oligonucleotide Arrays.- Meta-Analysis in Gene Expression Studies.- Practical Analysis of Genome Contact Interaction Experiments.- Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.- Variant Calling From Next Generation Sequence Data.- Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.- NGS-QC Generator: A Quality Control System for ChIP-seq and Related Deep Sequencing-Generated Datasets.- Operating on Genomic Ranges Using BEDOPS.- GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality.- Visualizing Genomic Data using Gviz and Bioconductor.- Introducing Machine Learning Concepts with WEKA.- Experimental Design and Power Calculation for RNA-Seq Experiments.- It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-Seq Experiments Using Quasi-Likelihood Methods in EdgeR.