Note 1: The Basic Data Skills Introduction to R workshop is a prerequisite.
Note 2: In this workshop we use expression data generated using Salmon; the training materials for that portion of the workflow was covered in the Advanced Topics Introduction to (bulk) RNA-seq using High-Performance Computing workshop.
| Time | Topic | Instructor |
|---|---|---|
| 09:00 - 9:15 | Introduction to Workshop | Radhika |
| 09:15 - 10:00 | R Refresher Session | Mary |
| 10:00 - 10:15 | Coffee | |
| 10:15 - 11:25 | Overview of DGE Analysis Workflow | Meeta |
| 11:25 - 12:15 | Setting up for DGE Analysis: Count Normalization | Jihe |
| 12:15 - 13:15 | Lunch | |
| 13:15 - 14:40 | Setting up for DGE Analysis: Count Data QC | Radhika |
| 14:40 - 15:10 | Overview of DESeq2 Methods | Mary |
| 15:10- 15:25 | Coffee | |
| 15:25 - 15:55 | Overview of DESeq2 Methods | Mary |
| 15:55 - 17:00 | DGE Analysis: Pairwise Comparisons (Wald Test) | Meeta |
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:15 | DGE Analysis: Workflow Summarization | Mary |
| 9:15 - 10:15 | DGE Analysis: Visualization | Radhika |
| 10:15 - 10:30 | Coffee | |
| 10:30 - 11:00 | DGE Analysis: Visualization (cont'd) | Radhika |
| 11:00 - 12:00 | DGE Analysis: Likelihood Ratio Test | Meeta |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:00 | Gene Annotations | Meeta |
| 14:00 - 14:30 | Functional Analysis | Jihe |
| 14:30- 14:45 | Coffee | |
| 14:45 - 16:15 | Functional Analysis (cont'd) | Mary |
| 16:15 - 17:00 | Wrap-up | Radhika |