Workshop Schedule
Below is a preliminary schedule for the 2024 August Introduction to Bulk RNA-Seq and Reproducible Research Practices Workshop. This schedule is subject to minor changes and will be updated with additional materials before the workshop.
The workshop will takes place from August 19-22 at the University of Minnesota. We will meet each day at 717 Delaware Street SE, Minneapolis, MN 55414 in Room 105.
Note: All times are CDT.
| Time | Topic |
|---|---|
| Day 1 | 2024-08-19 Intro to R and the Tidyverse Intro to Reproducible Research Practices |
| 8:30 AM | Arrive and check-in Breakfast and coffee available |
| 9:00 AM | Welcome, introductions and getting started Workshop intro slides (PDF) |
| 10:00 AM | Introduction to R and RStudio Intro to R and RStudio slides (PDF) |
| 11:15 AM | Coffee break |
| 11:30 AM | Introduction to ggplot2 |
| 12:30 PM | Lunch break |
| 1:30 PM | Introduction to the tidyverse |
| 2:30 PM | Coffee break |
| 2:45 PM | Questions and consultation time |
| Exercise: Introduction to base R | |
| Exercise: Introduction to R | |
Exercise: Introduction to the tidyverse, Part 1 |
|
Exercise: Introduction to the tidyverse, Part 2 |
|
| 3:30 PM | Introduction to reproducible research practices Intro to reproducible research practices slides (PDF) |
| 4:00 PM | Project organization Project organization slides (PDF) |
| 5:00 PM | Adjourn |
| Time | Topic |
|---|---|
| Day 2 | 2024-08-20 Reproducible Research Practices Intro to Bulk RNA-Seq |
| 8:30 AM | Breakfast and coffee available |
| 9:00 AM | Questions and review |
| 9:30 AM | Introduction to UNIX and the command line Intro to UNIX slides (PDF) |
| 10:30 AM | Coffee break |
| 10:45 AM | Introduction to Git / Forking and cloning Intro to Git slides (PDF) |
| 11:15 AM | Shell scripting Shell scripting slides (PDF) |
| 12:15 PM | Lunch break |
| 1:15 PM | The Git stage/commit/push workflow Git stage/commit/push slides (PDF) |
| 1:45 PM | Organizing code in scripts and notebooks Organizing code slides (PDF) |
| 2:30 PM | Managing packages and environments Managing environments slides (PDF) |
| 3:00 PM | Coffee break |
| 3:15 PM | Working with branches in Git Working with branches in Git slides (PDF) |
| 4:15 PM | Questions and consultation time |
| 5:00 PM | Adjourn |
| 5:30 PM | Group dinner at Surly Brewing Co. 520 Malcolm Ave SE, Minneapolis, MN 55414 |
| Time | Topic |
|---|---|
| Day 3 | 2024-08-21 Bulk RNA-Seq |
| 8:30 AM | Breakfast and coffee available |
| 9:00 AM | Introduction to bulk RNA-Seq Introduction to bulk RNA-seq slides (PDF) RNA-Seq quantification (trim, filter, quant) |
| 10:00 AM | RNA-Seq import with tximeta |
| 10:45 AM | Coffee break |
| 11:00 AM | RNA-Seq exploratory analysis |
| Time permitting Activity: Neuroblastoma cell line tximeta | |
| 12:00 PM | Lunch break |
| 1:00 PM | Set up Git on RStudio Server Git setup slides (PDF) |
| 1:30 PM | Differential expression analysis |
| 2:45 PM | Coffee break |
| 3:00 PM | Heatmaps and clustering |
| 4:00 PM | Questions and consultation time |
| Exercise: Exploratory data analysis | |
| Exercise: Bulk RNA-seq | |
| 5:00 PM | Adjourn |
| Time | Topic |
|---|---|
| Day 4 | 2024-08-22 Bulk RNA-Seq: Pathway Analysis Participant Presentations |
| 8:30 AM | Breakfast and coffee available |
| 9:00 AM | Questions and review |
| 9:30 AM | Introduction to pathway analysis Introduction to pathway analysis slides (PDF) |
| 10:00 AM | Over-representation analysis |
| 11:00 AM | Coffee break |
| 11:15 AM | Gene Set Enrichment Analysis (GSEA) Gene Set Variation Analysis (GSVA) |
| 12:30 PM | Lunch break |
| 1:30 PM | Questions and consultation time |
| Exercise: Over-representation analysis | |
| Exercise: Gene Set Enrichment Analysis (GSEA) | |
| Exercise: Gene Set Variation Analysis (GSVA) | |
| 3:00 PM | Participant presentations |
| 4:00 PM | Adjourn |