Bioinformatics workshop series: 8. Functional analysis using Gene Set Enrichment Analysis (GSEA) (In-Person)

Registration is required. Click here to register.

Session 8 – Functional analysis using Gene Set Enrichment Analysis (GSEA)

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 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 tutorial dataset will be made available to all registrants.
• You may also use your HPC account to access GSEA in Yale Open OnDemand.

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 analysis.

Date: Every Tuesday from February 6 until March 26

Time: from 10 am-12 pm

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.

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)