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---
title: "University of Alabama at Birmingham: July 09-10, 2024"
---
# UAB Biological Data Science Workshop
> University of Alabama at Birmingham
>
> July 09-10, 2024
>
> 8:00am - 5:00 pm CST
>
> **Instructors**: Austyn Trull, Bharat Mishra, Lara Ianov, Luke Potter, and Nilesh Kumar
>
> **Helpers**: Gurpreet Kaur, Kristen Coutinho, Samuel Bharti, Shaurita Hutchins, and Tarun Mamidi
>
> **Register now at [this link](https://events.uab.edu/en/6g1Y8if7/u-bds-bulk-rnaseq-workshop-4a2ePZuPa1/overview)**
## General Information
This event is a two-day example-driven hands-on workshop designed to teach introductory Bulk RNA Seq. The workshop will cover the following topics:
- Introduction to raw data management and data exploration.
- Secondary analysis with nf-core/rnaseq.
- Tertiary analysis including quality control, data normalization, gene annotation, gene enrichment analysis.
- Fundamentals of data visualization for transcriptomics and data interpretation.
This workshop is designed as a foundation upon which more specialized skills can be built, but will not delve into transcriptomics beyond bulk RNA-seq or other advanced topics in computational biology or software development. These topics will be covered in later workshops.
**Who:** The course is aimed at graduate students and other researchers. **No prior knowledge of RNA-seq analysis tools presented at this workshop is needed. However, it is heavily encouraged to have a level of familiarity with R and UNIX.**
**Where:** Heritage Hall Room 104 (1401 University Blvd, Birmingham, AL 35233)
**When:** July 09-10, 2024
**Requirements:** Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Please see the [installation instructions](installation.html) to ensure all required tools and packages are setup prior to the workshop.
If you have any questions or errors while installing any of the software or packages or during any of the setup, please attend one of the below sessions for troubleshooting. The dates and times for these more focused are listed below, and the Zoom link is available [here](https://uab.zoom.us/j/89923096971?pwd=pjpwOzRqMyoMrhU5872GhEu8XealEY.1).
- July 2nd: 2pm - 2:30pm
- July 8th: 11:30am - 12pm
**Accessibility:** We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
- The room is wheelchair / scooter accessible.
- Accessible restrooms are available.
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
**Contact:** Please email [kdaughtry\@uabmc.edu](mailto:kdaughtry@uabmc.edu) for more information
**Roles:** The roles for this workshop (who will be doing what) will be the same as the roles present in a Software Carpentries workshop. To learn more about the roles, refer the [the Software Carpentries Workshop FAQ](https://carpentries.org/workshop_faq/#what-are-the-roles-of-everyone-participating-in-a-workshop)
## Collaborative Notes
We will use this [Etherpad document](https://etherpad.wikimedia.org/p/uab-2024-07-09) for chatting, taking notes, and sharing URLs and bits of code
## Schedule
| Day 1 | | Day 2 | |
|----------------:|-----------------|----------------:|----------------------|
| 08:00 | Sign-in & Setup | 08:30 | Sign-in |
| 08:50 | Introduction & Welcome Session | 09:00 | Data Assumptions, DEG Analysis, and Annotation |
| 09:00 | Introduction to RNA-Seq Analysis | 10:30 | Morning Break |
| 09:30 | Introduction to nf-core rnaseq | 10:45 | Data Exploration and DEG Visualization |
| 10:30 | Morning Break | 12:15 | Lunch |
| 10:45 | Executing nf-core rnaseq | 13:00 | DEG Visualization (continued) |
| 12:00 | Lunch | 13:30 | Enrichment Analysis & Visualization |
| 12:45 | Reviewing RNASeq Results | 15:00 | Break |
| 14:00 | Break | 15:15 | GSEA Analysis & Visualization |
| 14:15 | Intro to DESeq2 and QC | 16:45 | Wrap-Up & Additional Resources |
| 17:00 | END | 17:00 | END |
## Installation Instructions
Please ensure you follow all instructions on [this page](installation.html).