May 7, 2014: in order to clean up and trim down the memory size of this repo, we've moved out non-code objects out of this repo. The celfiles and agilent folder of week2 has been moved to the rawdata repo.

May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/

March 30, 2014 : we are still adding R markdown files to this repository. Expect fully finished files for all weeks by second week of May 2014.

Week 1: Introduction

• What we measure and why
• R programming skills
• Probability distributions
• Exploratory data analysis

Week 2: Measurement technology

• Microarray technology
• Next generation sequencing technology
• Working with data in R

Week 3: Inference

• Inference
• Linear models

Week 4: Background correction and normalization

• Modeling
• Background
• Normalization

Week 5: Distance, clustering, and prediction

• Distance and clustering
• Prediction

Week 6: Batch effects

• Statistical solutions to batch effects
• Applying batch effects solutions

Week 7: Advanced differential expression

• Hierarchical modeling
• Multiple comparisons
• Gene set testing
• Gene and technology annotations

Week 8: Advanced topics

• Manipulating NGS data using Bioconductor
• Genome variation
• RNA sequencing
• DNA methylation
• ChIP sequencing