Differential Gene Expression Analysis Workshop

Note: Some HBC workshops are taught in person and others online via Zoom.

ONLINE Workshop dates and times:

Tuesday, March 18, 2025: 10 AM - 12 PM

Friday, March 21, 2025: 10 AM - 12 PM

Tuesday, March 25, 2025: 10 AM - 12 PM

Friday, March 28, 2025: 10 AM - 12 PM

Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!

NOTE: Workshop dates are subject to change.

Description:

This hands-on workshop will introduce participants to statistical methods and considerations utilized to perform differential gene expression analysis on bulk RNA-seq data. Participants will learn about best practices in quality control, how to perform statistical analysis to obtain lists of differentially expressed (DE) genes using DESeq2. The workshop will also give participants an overview of tools for functional analysis of DE genes and how to extract some biological meaning from large gene lists.

Prerequisites:

This is one of our advanced workshops, and requires registrants to have attended the following Basic workshop offered by our training team in the last 6-8 months:

Introduction to R

There is an expectation of participants to have some/all of the following programming knowledge:

Solid understanding of data structures and fluent implementation of basic syntax in R.
Ability to use functions regularly and can modify arguments when necessary.
Comfortable installing packages and troubleshooting issues.
Data wrangling expertise (subsetting vectors and data frames) using base R or tidyverse
Familiarity with ggplot2 for data visualization.

I am fluent in R but have not attended the HBC prerequisite workshop, can I still register?

Yes, please register and provide your R/programming exerience on the form, and we’ll get back to you.

Who should attend?

Eligible* Harvard researchers who have attended our Introduction to R workshop (or have working knowledge of R), and want to learn:

How to perform a differential expression analysis at the gene-level on bulk RNA-seq data
How to effectively use R to get your data in the appropriate format for DE analysis
The steps and statistical approaches used in assessing the quality of your abundance estimates (count data)
How to visualize expression patterns for differentially expressed genes
How to perform functional analysis on gene lists with R-based tools

Cost:

There is a non-refundable and non-transferable $65 registration fee for this advanced workshop.

We will be accepting 25 participants on a first-come, first-served basis:

If you are one of the first 25 eligible* registrants, you will receive an email within 1 week with a link to pay the (non-refundable & non-transferable) $65 registration fee.
If you are not among the first 25 eligible* registrants, you will be added to the waitlist and notified when we open registration for the next iteration of this workshop.

NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.

*NOTE: HMS Graduate Students may receive waivers on registration fees. Please register and we’ll followup with you.

Registration:

Please make sure you take the following into account when signing up for the workshop:

Mandatory attendance for all four classes.
3-5 hours of reading and exercises from selected lessons before each workshop sessions.
Active participation during discussion sessions.

(Registration opens 2 weeks before the start of advanced workshops.)

Eligibility requirements:

^*To be eligible to attend this workshop you should fulfill at least one of the following criteria:

Harvard Medical School researcher in a lab on the Quad, with grants administered by HMS Gordon Hall
Harvard School of Dental Medicine researcher, with grants administered by HMS Gordon Hall
Graduate student at the Harvard Medical School
Researcher affiliated with the Dana-Farber / Harvard Cancer Center (DF/HCC).
Researcher at a Harvard-affiliated institution participating in HIV related research.

If you are unsure of your eligibility, please register anyway and we will get back to you.

(Please check the eligibility requirements prior to registering)

NOTE: We do not record our training sessions.

Questions?

Please email us at hbctraining@hsph.harvard.edu with any questions.