Introduction to Differential Gene Expression Analysis
Note: Some HBC workshops are taught in person and others are online via Zoom. Please take note for scheduling purposes!
ONLINE Workshop dates and times:
Friday, November 14, 2025: 10 AM - 12 PM
Tuesday, November 18, 2025: 10 AM - 12 PM
Friday, November 21, 2025: 10 AM - 12 PM
Tuesday, November 25, 2025: 10 AM - 12 PM
NOTE: Workshop dates are subject to change.
Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!
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 12-24 months:
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?
Harvard-affiliated 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 registration fee for this advanced workshop*. After registering below, you will receive an email within 1 week with a link to pay.
Priority is given to Harvard Quad and DF/HCC researchers, who are subsidized for this workshop at a price of $65. Others interested in our workshops can find our prices here and should register below.
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.
Eligibility:
Priority is given to Harvard researchers:
- at the Harvard Medical School in a lab on the Quad, with grants administered by HMS OR
- at the Harvard School of Dental Medicine, with grants administered by HMS Gordon Hall OR
- an HMS graduate student OR
- affiliated with Dana-Farber / Harvard Cancer Center (DF/HCC)
If you are unsure of your eligibility, please register anyway and we will get back to you.
NOTE: We do not record our training sessions.
Questions?
Please email us at hbctraining@hsph.harvard.edu with any questions.