RNA-seq analysis with Bioconductor

Dana Farber Cancer Institute

Jul 31-Aug 1, 2023

9:00 am - 5:00 pm ET

Instructors: Jenny Drnevich, Sehyun Oh

Helpers: Maria Doyle, others TBC

General Information


Bioconductor Carpentries develops and teaches workshops on the fundamental data skills needed to conduct omics data analysis. Its target audience is experimental researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved.

Who: This lesson assumes you have a working knowledge of R and some previous exposure to RStudio. These requirements can be fulfilled by either:

  1. completing a Bioconductor Carpentries Introduction to R workshop
  2. independent exposure to R and RStudio

In addition, this lesson assumes that learners have some familiarity with RNA transcription and high-throughput sequencing.

Learner profiles of hypothetical attendees of the RNA-Seq workshop can be found on this page.

Participants should bring their own laptops and plan to participate actively.

Where: Smith Building, 1 Jimmy Fund Way, Boston, MA 02215. Get directions with OpenStreetMap or Google Maps.

When: Jul 31-Aug 1, 2023. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email drnevich@illinois.edu or maria.doyle@ul.ie for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Cost: $75 USD

Application: You can apply to attend workshop by filling out the form in the "Apply for a place" button below. Applications will be reviewed by the organisers until places are filled, and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful).

Code of Conduct

Everyone who participates in Bioconductor activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

Before starting Pre-workshop survey
Morning Workshop Overview
Introduction to RNA-seq
Experimental design
Afternoon Importing and annotating quantified data into R
Exploratory analysis and quality control
Evening END

Day 2

MorningDifferential expression analysis
AfternoonGene set analysis
Next steps
Evening Post-workshop survey

The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule.


To participate in a Bioconductor workshop workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the R/Bioconductor RNAseq workshop can be found at the workshop overview site.