All lectures of this course were recorded and can be found at YouTube.
- 09:00-09:45 Lecture: Introduction and experimental design (Jules Gilet) Video
- 09:45-10:15 coffee break
- 10:15-11:00 Lecture: Quality control (Åsa Björklund) Video
- 11:00-12:00 Labs: Quality control (Åsa & Jules). Bonus exercise (not to be done in the class): Sequencing QC and Ikura pipeline (Jules).
- 12:00-13:00 lunch
- 13:00-13:45 Lecture: Normalisation and removal of confounding factors (Heli Pessa & Bishwa Ghimire) Video Video
- 13:45-14:30 Labs: Normalisation and removal of confounding factors (Heli & Bishwa)
- 14:30-15:00 coffee break
- 15:00-15:45 Lecture: Data integration (Ahmed Mahfouz) Video
- 15:45-17:00 Labs: Data integration (Ahmed Mahfouz)
- 09:00-09:45 Dimensionality_reduction (Paulo Czarnewski) Video
- 09:45-10:15 coffee break
- 10:15-11:00 Labs: Continue from Data integration, (Rmd file)
- 11:00-12:00 Lecture: Clustering (Ahmed Mahfouz) Video
- 12:00-13:00 lunch
- 13:00-14:30 Labs: Clustering, (Rmd file) (Ahmed Mahfouz)
- 14:30-15:00 coffee break
- 15:00-17:00 Differential expression, (Rmd file 1), (Rmd file 2) (Ståle Nygård) Video
- 09:00-11:00 Lecture: Cell type identification (Philip Lijnzaad) Video
- 09:45-10:15 coffee break
- 10:15-11:00 Labs: Cell type identification, (Rmd file) (Philip)
- 11:00-12:00 Lecture: Trajectories/Pseudo-time I (Paulo, Jules). Video Labs
- 12:00-13:00 lunch
- 13:00-14:00 Trajectories/Pseudo-time II (Paulo, Jules). Labs
- 14:00-14:30 Lecture: Spatial transcriptomics I (Lars Borm) Video
- 14:30-15:00 coffee break
- 15:00-16:30 Lecture: Spatial transcriptomics II (Lars Borm & Jeongbin Park) Video
- 16:30-17:00 Discussion and questions
- launch the Conda environment on the classroom computers
- access the virtual machine image in the cPouta cloud
- install the Conda environment on your own computer after the course
- Åsa Björklund (NBIS, ELIXIR-SE, Sweden)
- Paulo Czarnewski (NBIS, ELIXIR-SE, Sweden)
- Ahmed Mahfouz (LUMC, Netherlands)
- Ståle Nygård (UIO, Norway)
- Jeongbin Park (Charité-Universitätsmedizin Berlin and de.NBI, Germany)
- Lars Borm (Karolinska Institutet, Sweden)
- Jules Gilet (Institut Curie, France)
- Heli Pessa (University of Helsinki, Finland)
- Bishwa Ghimire (FIMM, Finland)
- Philip Lijnzaad (Princess Maxima Center for Pediatric Oncology, Netherlands)
- Content: eija.korpelainen@csc.fi
- Practicalities: event-support@csc.fi