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single-cell-RNAseq-R-2018

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)
Price:
  • 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
Content: chipster@csc.fi
Practicalities: event-support@csc.fi

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

 

Prerequisites:

  • 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