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

Time: Wednesday 14:15 - 16:00 over Zoom


No.  Date Teacher Title Code, Datasets
1 03.03.2021 Julien Lecture scope and prerequisites / Revision of R basics
2 10.03.2021 Robert Bioconductor and data types packages_to_install.R, gencode.v28.annotation.1.1.10M.gtf, gencode.v28.transcripts.1.1.10M.fa
3 17.03.2021 Pan mRNASeq 1: overview, quantification (salmon/tximeta )
4 24.03.2021 Charlotte mRNASeq 2: GenomicRanges, SummarizedExperiment, annotation, visualization (PCA, …) packages_to_install.R
5 31.03.2021 Robert mRNASeq 3: Differential Gene Expression with DESeq2 packages_to_install.R
6 07.04.2021 Julien mRNASeq 4: another example (complex design, batch correction using covariate) filereport_read_run_PRJNA255258_tsv.txt, SE.rds, SEG.rds
7 14.04.2021 Florian Exam 1
8 21.04.2021 Charlotte Single cell mRNASeq 1: overview, QC, filtering, dimensionality reduction, visualization, SingleCellExperiment packages_to_install.R
9 28.04.2021 Pan Single cell mRNASeq 2: batch correction, clustering, differential gene expression packages_to_install.R
10 05.05.2021 Michael ChIPSeq 1: Introduction and simulation packages_to_install.R, 10_ChIPseq_coverage_interactive.Rmd, 10_ChIPseq_coverage_shinyApp.R
11 12.05.2021 Michael ChIPSeq 2: Analysis workflow packages_to_install.R, 11_ChIPseq_2.R, ChIP_promoter_counts.rds
12 19.05.2021 Florian ATACSeq: QC, peak finding, differential accessibility packages_to_install.R, alignments.tsv, check data on nextcloud!
13 26.05.2021 Florian Motifs: PWMs, prediction, motif enrichment packages_to_install.R, GATA2_binding_sites.rds, merged_peaks_TFH_TH1.tsv.gz, jaspar2018_mm_binary.rds
14 02.06.2021 Robert Exam 2

Download Calendar ICS file for this lecture series.


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 installation

It is recommended to have an up-to-date installation of R on your computer (i.e., R version >= 4.0.0, available here). 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.

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:

Note that an outdated version of R will be problematic for the course!

For people with an existing sciCORE account:

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