Bioinformatics workshop series: 7. Functional analysis using R (In-Person)
Registration is required. Click here to register.
Session 7 – Functional analysis using R
Presenter: Dr. Bony De Kumar, Yale Center for Genomic Analysis
Series Details: see below
Summary: Explore the power of R for functional analysis in RNAseq studies. This hands-on workshop guides participants through using R for insightful data interpretation, covering various techniques and tools for effective transcriptomic functional analysis.
You will learn how to:
- Learn to use Bioconductor packages such as clusterprofiler, Pathview, and SPIA for GO and KEGG pathway analysis
- Learn to construct Dot plots, Bra plots, Cnet Plots, and Emma Plots from Pathway enrichment data
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.
This session is suitable for both beginner and intermediate users.
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.
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