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. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
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