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Single cell RNA-seq data analysis with R
Date: 27.05.2019 9:00 - 29.05.2019 17:00
Location details: The event is organised at the CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. The best way to reach us is by public transportation; more detailed travel tips are available.
Language: English
Lecturers: Åsa Björklund (NBIS ELIXIR-SE)
Paulo Czarnewski (NBIS ELIXIR-SE)
Ahmed Mahfouz (LUMC)
Ståle Nygård (UIO)
Olga Dethlefsen (NBIS ELIXIR-SE)
Lars Borm (Karolinska Institutet)
Jules Gilet (Institut Curie)
Heli Pessa (University of Helsinki)
Bishwa Ghimire (FIMM)
Philip Lijnzaad (Princess Maxima Center for Pediatric Oncology)
Jeongbin Park (Charité-Universitätsmedizin Berlin & de.NBI)
Rui Benfeitas (NBIS ELIXIR-SE)
Dawit Yohannes (University of Helsinki)
  • Free for Finnish universities, universities of applied sciences and governmental research institutes.
  • Free for others.
Morning and afternoon coffees are included in the course.
Registration is closed.
Participants are selected based on their motivation description, and we will also do our best to ensure that every country / research group gets at least one representative in the course. It is therefore important that in the application form you describe your need for the course (remember to indicate if you already have scRNA-seq data or if you are planning a scRNA-seq experiment) and indicate your R experience and the name of the group leader. All the applicants were informed about the selection results on 18.4.2019. If you didn't receive an email from us, please check your spam folder.
Additional information

This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE project.

In order to participate in this course you should have prior experience in using R.


More detailed schedule will be published soon. Every course day is 9:00-17:00.

Monday 27.5.2019

  • Introduction and experimental design (Åsa Björklund, Jules Gilet)
  • QC, data preprocessing (Åsa Björklund)
  • Normalisation and removal of confounding factors (Heli Pessa, Bishwa Ghimire)
  • Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)

Tuesday 28.5.2019

  • Dimensionality reduction (PCA, tSNE and UMAP) (Paulo Czarnewski)
  • Clustering (Ahmed Mahfouz)
  • Differential gene expression analysis (Ståle Nygård and Olga Dethlefsen)

Wednesday 29.5.2019

  • Cell type identification (Philip Lijnzaad)
  • Trajectories/Pseudo-time (Paulo Czarnewski)
  • Spatial transcriptomics (Jeongbin Park and Lars Borm)
  • Discussion and wrap-up

Learning objectives

After this course you will be able to:

  • use a range of bioinformatics tools to analyze single cell RNA-seq data
  • discuss a variety of aspects of single cell RNA-seq data analysis
  • understand the advantages and limitations of single cell RNA-seq data analysis


Projects and Collaboration Networks
Service Break
Projects and Collaboration Networks
Service Break