Bioinformatics Workshop Series - Session 2: Find, Download and Transform public bulk RNA seq data to analyze with DESeq2 in RStudio
Bioinformatics Workshop Series - Session 2: Find, Download and Transform public bulk RNA seq data to analyze with DESeq2 in RStudio In-Person
Registration Required
Workshop Series: Introduction to bulk RNA-seq analysis - from counts to functional analysis
Summary:
The Bioinformatics Support Hub has designed this hands-on teaching series for researchers interested in learning the basics steps for re-analysis of publicly available bulk-RNAseq data. Over the next two months, you can learn basic concepts concerning genomic data annotation and vocabulary, where to find bulk RNAseq data to re-analyze, how to perform differential gene analysis in RStudio and with point-click proprietary software, how to visualize your results, how to find transcription factors that may be regulating differentially expressed genes, and finally different approaches to perform gene pathway analysis. *Registrations for October sessions will open at the end of September.
Session 2. Find, Download and Transform public bulk RNA seq data to analyze with DESeq2 in RStudio
Transcriptomic data is increasingly available in public repositories making it easier for reanalysis. Join us for the first part on how to search publicly available transcriptomic data, download and prepare it to run a differential gene expression analysis using *DESeq2* R package
You will learn how to:
- Search and download bulk RNA-seq data available on GREIN - GEO RNA-seq Experiments Interactive Navigator
- Process GREIN data tables to be analyzed by DESeq2 in RStudio
- Load R packages (e.g. DESeq2)
- Setup data to run DESeq2
Requirements:
- Bring a laptop with R and RStudio installed and running.
Details:
Target audience: These classes are meant to novices in bulk RNAseq analysis, with none to minimal knowledge in R programming.
Seating – in person classes are limited to 16 places.
Registrations - open to all interested. However, seating will be on “first come, first served” basis.
Recording – we will record the sessions so you can follow asynchronously.
Series Program:
|
Date |
Session |
Mode |
Presenter |
|
9/14/23 |
Session 1 - Intro to annotation of gene expression data |
In-person |
Rolando Milian |
|
9/21/23 |
Session 2 - Find, Download and Transform public bulk RNA seq data to analyze with DESeq2 in RStudio |
In-person |
Sofia Fertuzinhos |
|
9/28/23 |
Session 3 - Upload bulk RNAseq data tables into RStudio and setup a DESeq2 analysis |
In-person |
Sofia Fertuzinhos |
|
10/5/23 |
Session 4 - Manipulate DESeq2’s results() and plot functions |
In-person |
Sofia Fertuzinhos |
|
10/12/23 |
Session 5 – DEMO - Analyzing and Visualizing RNAseq public dataset using Qlucore Omics Explorer |
Online |
Yana Stackpole - Qlucore |
|
10/19/23 |
Session 6 – DEMO - Transcription factors analysis with TRANSFAC |
Online |
Volker – Transfac |
|
10/24/23 |
Session 7 - Functional analysis of omics data: Overrepresentation Analysis ORA |
In-person |
Rolando Milian |
|
10/26/23 |
Session 8 - Gene Set Enrichment Analysis GSEA |
In-person |
Rolando Milian |
- Date:
- Thursday, September 21, 2023
- 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
