Bioinformatics workshop series: 3. Introduction to the Yale Clusters and Open OnDemand
Bioinformatics workshop series: 3. Introduction to the Yale Clusters and Open OnDemand In-Person
Session 3 – Introduction to the Yale Clusters and Open OnDemand
Registration required* and In-Person
Presenter: Dr. Robert Bjornson, Yale Center for Research Computing
Series Details: see below
Summary: A general introduction to Yale's HPC resources, which will be used for RNAseq analysis in subsequent sessions. This session introduces basics of cluster usage, as well as tools like Open OnDemand, Jupyter, and Conda.
You will learn:
- Overview of High Performance Computing resources (clusters) at Yale
- How to log into the clusters
- How to run jobs on the clusters
- How to get help
Requirements:
- There will be a hands-on component; please bring a computer. You will only need a browser.
- Date:
- Tuesday, February 20, 2024
- Time:
- 10:00am - 12:00pm
- Time Zone:
- Eastern Time - US & Canada (change)
- Location:
- SHM L 115, 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
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 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 |
