Statistical Bioinformatics
Statistics 5820/6820, Spring 2006
Instructor: John R. Stevens
Summer course:
Bioinformatics: Problems and Solutions
Course Documents
Unit 1: Getting Started
- R: The R Project
- CRAN: The Comprehensive R Archive Network
- Introduction to R: A good resource for most uses of R
- Bioconductor Project: Free R packages for the analysis of genomic data
- R reference card: Tom Short's ''cheat sheet'' for R commands
- Notes for Installing and Using R (for 1/11/06 class)
- Notes (slides) for introduction to microarray technology (for 1/18/06 class)
- From 1/18/06 slides: Animation 1 --- Animation 2
- Good journals to watch:
- Lockhart paper: a good review of technology
- Notes for going from image to meaningful data (for 1/20/06 class)
Unit 2: Design and Preprocessing
- Notes for microarray experimental design (for 1/25/06 class)
- Notes for preprocessing with MAS 5.0 (for 2/1/06 class)
- Notes for preprocessing with dChip and vsn (for 2/6/06 class)
- Notes for preprocessing with RMA and GCRMA (for 2/8/06 class)
- Notes for quality checks for microarray data (for 2/10/06 class)
Unit 3: Inference
- Notes for distance measures in microarray data (for 2/15/06 class)
- Notes for clustering and visualization in microarray data (for 2/17/06 class)
- Notes for intro. to multiple testing with microarray data (for 2/27/06 class)
- Notes for intro. to filtering with microarray data (for 3/3/06 class)
- Notes for intro. to differential expression tests with microarray data (for 3/10/06 class)
- Notes for reporting lists of candidate genes (for 3/24/06 class)
Unit 4: Sequence Analysis
- Notes for intro. to protein pairwise alignment and phylogenetic trees (for 3/27/06 class)
- Notes for intro. to BLAST (for 4/3/06 class)
- Notes for intro. to Hidden Markov Models and profiles in sequence alignment (for 4/07/06 class)
Unit 5: Student Presentations