Analysis of Genomics Data with R/Bioconductor (Spring 2025)
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 | 19.02.2025 | Athimed | Lecture scope and prerequisites / Revision of R basics | Biozentrum, Seminarraum U1.191 | |
| 2 | 26.02.2025 | Athimed | Bioconductor and data types | Biozentrum, Seminarraum U1.191 | |
| 3 | 05.03.2025 | Charlotte | mRNASeq 1: Overview, quantification (salmon/tximeta) |
Biozentrum, Seminarraum U1.191 | |
| 12.03.2025 | Fasnachstferien | ||||
| 4 | 19.03.2025 | Pan | mRNASeq 2: GenomicRanges, SummarizedExperiment, annotation, visualization (PCA, …) |
Biozentrum, Seminarraum U1.191 | |
| 5 | 26.03.2025 | Robert | mRNASeq 3: Differential Gene Expression with DESeq2 |
Biozentrum, Seminarraum U1.191 | |
| 6 | 02.04.2025 | Pan | Single cell mRNASeq 1: overview, QC, filtering, dimensionality reduction, visualization, SingleCellExperiment |
Biozentrum, Seminarraum U1.191 | |
| 7 | 09.04.2025 | Florian | Exam 1 | Biozentrum, Seminarraum U1.191 | |
| 8 | 16.04.2025 | Anastasiya | Single cell mRNASeq 2: batch correction, clustering, differential gene expression | Biozentrum, Seminarraum U1.191 | |
| 9 | 23.04.2025 | Anastasiya | Introduction to spatial transcriptomics | Biozentrum, Seminarraum U1.191 | |
| 10 | 30.04.2025 | Michael | ChIPSeq 1: Introduction and simulation | Biozentrum, Seminarraum U1.191 | |
| 11 | 07.05.2025 | Michael | ChIPSeq 2: Analysis workflow | Biozentrum, Seminarraum U1.191 | |
| 12 | 14.05.2025 | Florian | ATACSeq: QC, peak finding, differential accessibility | Biozentrum, Seminarraum U1.191 | |
| 13 | 21.05.2025 | Michal | Motifs: PWMs, prediction, motif enrichment | Biozentrum, Seminarraum U1.191 | |
| 14 | 28.05.2025 | 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 >= 4.4.2, 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Note that an outdated version of R will be problematic for the course!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 Cisco client
- Go to https://ood.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:
- Go to https://posit.cloud/ and create an account there
Copyright
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License, unless otherwise indicated.
The material represents a collaborative development effort by Anastasiya Börsch, Lukas Burger, Sarah Carl, Athimed El Taher, Florian Geier, Robert Ivanek, Panagiotis Papasaikas, Julien Roux, Helene Royo, Atul Sethi, Charlotte Soneson, Adam Alexander Thil Smith and Michael Stadler (listed in alphabetic order).