Analysis of Genomics Data with R/Bioconductor (Spring 2026)

 

45038-01 – Lecture with exercises (2 CP) / Vorlesung mit Übungen (2 KP)

Wednesdays 14:15 - 16:00 (Biozentrum, Seminarraum U1.191)

 

No. Date Teacher Title Room Code, Datasets
1 18.02.2026 Igor Lecture scope and prerequisites / Revision of R basics Biozentrum, Seminarraum U1.191  
  25.02.2026   Fasnachstferien    
2 04.03.2026 Athimed Bioconductor and data types Biozentrum, Seminarraum U1.191  
3 11.03.2026 Pan mRNASeq 1: Overview, quantification (salmon/tximeta) Biozentrum, Seminarraum U1.191  
4 18.03.2026 Pan mRNASeq 2: GenomicRanges, SummarizedExperiment, annotation, visualization (PCA, …,) Biozentrum, Seminarraum U1.191  
5 25.03.2026 Robert mRNASeq 3: Differential Gene Expression with DESeq2 Biozentrum, Seminarraum U1.191  
6 01.04.2026 Charlote Single cell mRNASeq 1: overview, QC, filtering, dimensionality reduction, visualization, SingleCellExperiment Biozentrum, Seminarraum U1.191  
7 08.04.2026 Florian Exam 1 Biozentrum, Seminarraum U1.191  
8 15.04.2026 Anastasiya Single cell mRNASeq 2: batch correction, clustering, differential gene expression Biozentrum, Seminarraum U1.191  
9 22.04.2026 Anastasiya Introduction to spatial transcriptomics Biozentrum, Seminarraum U1.191  
10 29.04.2026 Michael ChIPSeq 1: Introduction and simulation Biozentrum, Seminarraum U1.191  
11 06.05.2026 Michael ChIPSeq 2: Analysis workflow Biozentrum, Seminarraum U1.191  
12 13.05.2026 Florian ATACSeq: QC, peak finding, differential accessibility Biozentrum, Seminarraum U1.191  
13 20.05.2026 Michal Motifs: PWMs, prediction, motif enrichment Biozentrum, Seminarraum U1.191  
14 27.05.2026 Robert Exam 2 Biozentrum, Seminarraum U1.191  

You can download ICS Calendar file for this lecture series and import it in your calendar app.

Course Prerequisite

A basic knowledge of R is required for this course!
Review the content of lectures from the Introduction to R course before signing up.

R – Local Installation

  • It is recommended to have an up-to-date installation of R on your computer.
    Currently R version >= 4.5.2, available here.
    Note that an outdated version of R will be problematic for the course!
  • Together with it, we strongly recommend to have Rstudio installed too.
    If you have limited rights to install software on your computer, please contact your ITs before the course.

R – Rstudio Server

If a local installation is not possible on your computer, there is the possibility to use Rstudio server, a browser-based interface to a version of R running on a remote server. Here are the different options:

  • For people with an existing sciCORE account:
    • If not at the University, connect to University VPN using the Palo Alto Global Protect client
    • Go to https://ood-ubuntu.scicore.unibas.ch
    • Log in with your Unibas username and password
  • For FMI members:
    • If not at the FMI, connect to VPN using the PulseSecure client
    • Go to http://rstudio.fmi.ch
    • Log in with your FMI username and password
  • Others:

R – Docker

It is possible to run R and RStudio inside a docker container. This option is useful in case conflicts in your current operating system prevent you from installing R or other packages required for the course.

  1. Setup
    • Install Docker Desktop on your computer (Administrator rights are required).
    • Download the image: Open your terminal and run: docker pull bioconductor/bioconductor_docker:RELEASE_3_21-r-4.5.2. Alternatively search for bioconductor/bioconductor_docker in Docker Desktop GUI, hover over the name in the results and in dropdown menu Tag choose RELEASE_3_21-r-4.5.2. Image size is around 6 GB.
  2. Initial Launch (First Time Only)

    • By default, the container cannot see your computer’s files. To grant access to a specific folder, use the -v (volume) flag when launching.

    • Replace the <local-path> in the following command with the full path to the folder on your computer and <directory-name> with how you want the folder to appear inside RStudio:

      docker run -p 8787:8787 --name genomics_r -e PASSWORD=temp -v <local-path>:/home/rstudio/<directory-name> bioconductor/bioconductor_docker:RELEASE_3_21-r-4.5.2

    • Run the command.

  3. Access the RStudio
  4. Install required packages
  5. Stopping the container
    • When you are finished with your session, stop the container to free up your computer’s resources.
    • Command Line: docker stop genomics_r
    • Docker Desktop GUI: Go to the Containers tab and click the Stop (square) icon next to genomics_r
  6. Resuming your work
    • The next time you want to use RStudio, do not use docker run. Instead, simply start the existing container. All your installed packages will still be there.
    • Command Line: docker start genomics_r
    • Docker Desktop GUI: Go to the Containers tab and click the Start (play) icon next to genomics_r