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Projects and Collaboration Networks
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Single cell RNA-seq data analysis
Date: 21.09.2018 9:00 - 21.09.2018 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: Dawit Yohannes (University of Helsinki)
Bishwa Ghimire (FIMM)
Heli Pessa (University of Helsinki)
  • Free for Finnish universities, polytechnics and governmental research institutes.
  • Free for others.
All materials, lunches as well as morning and afternoon coffees are covered.
The seats are filled in the registration order. Please note, that there is usually a queue for the course, so in case you need to cancel your participation, do it as soon as possible to enable others to take your place.
Additional information

This one day hands-on course introduces the participants to single cell RNA-seq data analysis concepts and tools.

  • overview of preprocessing: from raw sequence reads to expression matrix
  • overview of popular tools and R packages for scRNAseq data analysis
  • scRNAseq data quality control
  • cluster analysis
    • removal of undesired sources of variation
    • variable gene detection
    • dimensionality reduction
    • clustering
  • cell type identification
    • using known markers
    • using automatic classification algorithms
  • differential gene expression analysis
  • pseudotime analysis
  • if time permits: Integrating different datasets (CCA in Seurat)


You will learn:

  • to assess the quality of scRNAseq data
  • to control batch effects and other unwanted variation
  • cell clustering and identification
  • differential gene expression analysis
  • choosing the tools for further analyses



  • some experience in using R
  • understanding of the basic principles of single cell RNA-seq experiments


Registration will open on this page in late August.

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