| Lectures | Links | Datasets | Class Info |
|---|
| Number | Date | Lecture Title | Resources | Description |
| Lecture 1 | 3/26/2013 | Introduction | ||
| Lab 1 | 3/28/2013 | Introduction to R | [PDF],[R] | We will cover an introduction to R, including data structure and management. |
| Lecture 2 | 4/2/2013 | Statistics: Testing and Inference | [PDF],[Video] | Illustrative example: Differential Expression Analysis with Microarrays |
| Lab 2 | 4/4/2013 | R: Testing and Inference | [R] | Differential Expression Analysis using R |
| Lecture 4A | 4/9/2013 | Microarray technologies | [PDF] | Background on microarrays technologies |
| Lecture 4B | 4/9/2013 | Sequencing technologies | [PDF], [Video] | Background on sequencing technologies |
| Lab 3 | 4/11/2013 | Sequencing file formats and R | [R] | Exercises for sequencing data |
| Lecture 5A | 4/16/2013 | Distance and Clustering | [PDF], [Video] | Popular methods for clustering genomics experiments |
| Lecture 5B | 4/16/2013 | Useful Plots | [PDF],[Video] | Examples of plots using in genomics data...and not so useful ones |
| Lab 4 | 4/18/2013 | Downloading Data | [R] | Downloading data from GEO and data cleaning |
| Lecture 6A | 4/23/2013 | Microarray Background Correction | [PDF] | How background signal influences microarray intensities |
| Lecture 6B | 4/23/2013 | Normalization | [PDF],[Video] | Normalization of expression arrays |
| Lab 5 | 4/25/2013 | Annotating variants | See 'Data' Below | Tools for annotating variants |
| Lecture 7 | 4/30/2013 | Advanced Differential Expression | [PDF] ,[Video] | More advanced methods for determining differential expression in high-throughput experiments |
| Lab 6 | 5/2/2013 | Differential expression in R | [R] | Performing differential expression analysis in R using limma |
| Lab 7 | 5/7/2013 | Analzying RNAseq in R | [R] | Using R to analyzed RNAseq data from alignment files |
Data-sets:
Links:
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