Bioinformatics workshop series: 6. Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio.
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Bioinformatics workshop series: 6. Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio. In-Person
Session 6 – Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio.
Registration required* and In-Person
Presenter: Dr. Sofia Fertuzinhos, Bioinformatics Support Hub, CWML
Series Details: see below
Summary: In this session, we will teach you the basics of analyzing bulk RNA-seq data using the open-source software RStudio (download from here) and the popular package "DESeq2". Specifically, we will focus on performing differential gene expression analysis, which involves identifying genes that are differentially expressed between two or more conditions.
You will learn how to:
- Import data files into RStudio
- Load R packages
- Run “DESeq2”
- Save processed data files into your computer (e.g. normalized counts, DEX genes table)
- Perform basic data visualization (e.g. PCA plot, MA plot)
Requirements:
Bring a laptop with R and RStudio installed and running (download from here). You may also use your
HPC account to access R/RStudio in Yale Open OnDemand.
- Date:
- Tuesday, March 12, 2024
- Time:
- 10:00am - 12:00pm
- Time Zone:
- Eastern Time - US & Canada (change)
- Location:
- SHM L 111, Cushing/Whitney Medical Library, 333 Cedar Street
- Campus:
- Medical School
- Categories:
- Bioinformatics
Bioinformatics workshop series: Intro to bulk RNA-seq data analysis: from experimental design to pathway analysis
Registration required* and In-Person
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 startperforming 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 |
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