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