RNA-seq analysis with Bioconductor

Karolinska Institutet, Stockholm, Sweden;

July 11-12, 2024

9:00 - 16:00 (CET)

Instructors: Rodrigo Arcoverde Cerveira da Silva

Helpers: Gustav Joas, Matthew Hinchcliff

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: Solnavägen 30, 171 64 Solna. Get directions with OpenStreetMap or Google Maps.

When: July 11-12, 2024. 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 rodrigo.arcoverde@ki.se or rodrigo.arcoverdi@gmail.com for more information.

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

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.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


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 (30 min)
Introduction to RNA-seq (1 hr)
Experimental Design (1 hr)
RStudio Project and Experimental Data (1 hr)
Afternoon Import and Annotation of Quantified Data in R (1.5 hr)
Exploratory Analysis and Quality Control (1.5 hr)
Evening END

Day 2

MorningDifferential Expression Analysis (2 hr)
AfternoonGene Set Enrichment Analysis (GSEA and ORA) (1.5 hr)
Next Steps (1 hr)
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 organizers if you would like more information about the planned schedule.


To participate in this workshop, you will need access to the software described below. Additionally, you will need an up-to-date browser.

We maintain a list of common installation problems as a reference for instructors, which can be useful on the Configuration Problems and Solutions wiki page.

Please check the “Summary and Setup” page by clicking HERE to be directed to the lesson site for instructions on how to obtain the software and data needed to follow the lesson. If you want to download the .Rmd files that contain both the scripts in “R chunks” and the texts formatted in markdown, access this folder on Google Drive and download both the .Rmd, the slides, and the data used for analysis.