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

Time: Wednesday 14:15 - 16:00

Venue: Biozentrum, Seminarraum 104

No. Date Teacher Exercises Title Code, Datasets
1 20.02.2019 Julien Pan Revison of R basics mice_data.csv, secretin.csv
2 27.02.2019 Charlotte Julien Bioconductor and data types packages_to_install.R, gencode.v28.annotation.1.1.10M.gtf, gencode.v28.transcripts.1.1.10M.fa
3 06.03.2019 Charlotte Lukas Annotation packages
4 13.03.2019 Fasnachtsferien
5 20.03.2019 Pan Charlotte Overview of RNAseq packages_to_install.R
6 27.03.2019 Atul Pan RNASeq 1: fastq -> counts 06_counts.txt, 03_counts.txt, 03_counts_st.txt
7 03.04.2019 Robert Atul RNASeq 2: counts -> DE 06_counts.txt, 03_counts.txt
8 10.04.2019 Julien Florian Exam 1 and recap exercise DGEList object
9 17.04.2019 Pan Charlotte Single cell mRNASeq umi_counts, read_counts, experiment_annotation, gene_annoation, exercise_data
10 24.04.2019 Florian Pan Genomic Ranges plotRanges.R
11 01.05.2019 Tag der Arbeit
12 08.05.2019 Michael Julien ChIPSeq 1 12_ChIPseq_coverage_interactive.Rmd, 12_ChIPseq_coverage_shinyApp.R
13 15.05.2019 Michael Florian ChIPSeq 2 ChIP_promoter_counts.rds
14 22.05.2019 Michael Pan ChIPSeq and mRNAseq ChIPdata_2kb_chr19.rds,ChIPdata_promoters.rds,ChIPdata_geneBodies.rds
15 29.05.2019 Florian Lukas Exam 2 and solution

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

For this course you will need an up-to-date installation of R (i.e., R version >= 3.5.0). Here is where you can download it: https://cran.r-project.org/.

Together with it, we strongly recommend to have Rstudio installed too: https://www.rstudio.com/products/rstudio/download/#download.

If you have limited rights to install softwares on your computer, please contact your ITs. Note that an outdated version of R will be problematic for the course!

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

For people with a sciCORE account*

* This is an account for the center for scientific computing of the Unibas, which needs to requested directly to them.

For FMI members

  • Log in to the eduroam network using yourFMIusername@fmi.ch
  • Connect to the VPN using the PulseSecure client
  • Go to http://rstudio.fmi.ch
  • Log in with your FMI username and password
  • Last year, some FMI members had problem connecting to the internet using eduroam, or did not know how to use the VPN. Please check with your ITs.