Bioinformatics workshop series: 8. Functional analysis using Gene Set Enrichment Analysis (GSEA)
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Bioinformatics workshop series: 8. Functional analysis using Gene Set Enrichment Analysis (GSEA) In-Person
Session 8 – Functional analysis using Gene Set Enrichment Analysis (GSEA)
Registration required* and In-Person
Presenter: Rolando Garcia-Milian, Bioinformatics Support Hub, CWML
Series Details: see below
Summary: Gene Set Enrichment Analysis (GSEA) (UC San Diego/Broad Institute) determines whether a set of genes shows statistically significant differences between two biological conditions (e.g., phenotypes). From this session/workshop you will learn how to run GSEA on your own datasets using the GSEA desktop application. During the session we will use a tutorial dataset that will be made available to all the registrants.
You will learn how to:
- Prepare your data and files for running GSEA.
- Use the Molecular Signature Database (MSigDB).
- Run GSEA analysis and the Leading-edge analysis and results interpretation.
- Send and visualize the results using the Enrichment Map app.
This session is suitable for both beginner and intermediate users of GSEA.
Prerequisites:
- Download and install the GSEA desktop version on your laptop.
- Download and install Cytoscape software
- A tutorial dataset will be made available to all registrants.
-
You may also use your HPC account to access GSEA in Yale Open OnDemand.
- Date:
- Tuesday, March 26, 2024
- Time:
- 10:00am - 12:00pm
- Time Zone:
- Eastern Time - US & Canada (change)
- Location:
- SHM L E26/E27, Cushing/Whitney Medical Library, 333 Cedar St
- Campus:
- Medical School
- Categories:
- Bioinformatics
Bioinformatics workshop series: Intro to bulk RNA-seq data analysis: from experimental design to pathway analysis
GENERAL DESCRIPTION: This workshop series offers an introduction to bulk RNA-seq data analysis, guiding participants through each step, from library preparation to gene set enrichment analysis. The series is composed of 8 sessions (see table below). The sessions will be led by field experts from the Yale Centers for Genomic Analysis (YCGA), Computational Research (YCRC) and Cushing/Whitney Medical Library Bioinformatics Support Hub to better connect you with bioinformatics services available at Yale.
We have structured this series in such a manner as to provide practical skills in experimental design, data processing, and functional analysis. The series is ideal for those new to the field of transcriptomics or those wanting to start performing their own analysis.
Date: Every Tuesday from February 6 until March 26
Time: from 10am-12pm
Requirements: No previous command line experience required.
Seating Information: For registered participants, seating operates on a first-come, first-served basis. Please ensure timely arrival to secure your seat.
*Registrations for March sessions will open at the end of February.
|
DATE |
SESSION |
MODE |
PRESENTER |
|
2/06/24 |
Session 1 - Foundations of Bulk-RNAseq Library Preparation |
In-person |
Bony De Kumar, PhD |
|
2/13/24 |
Session 2 - Considerations for Designing Next-Generation Sequencing Experiments |
In-person |
Francesc Lopez Giraldez, PhD |
|
2/20/24 |
Session 3 - Introduction to the Yale Clusters and Open OnDemand |
In-person |
Robert Bjornson, PhD |
|
2/27/24 |
Session 4 - RNAseq Data Processing: A Step-by-Step Guide from raw sequences to counts |
In-person |
Francesc Lopez Giraldez, PhD |
|
3/05/24 |
Session 5 – Streamlining RNAseq Analysis with the YCGA Pipeline |
In-person |
Francesc Lopez Giraldez, PhD |
|
3/12/24 |
Session 6 – Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio. |
In-person |
Sofia Fertuzinhos, PhD |
|
3/19/24 |
Session 7 - Functional analysis using R |
In-person |
Bony De Kumar, PhD |
|
3/26/24 |
Session 8 - Functional analysis using Gene Set Enrichment Analysis (GSEA) |
In-person |
Rolando Milian, MLS |
Event Organizer
