Topic outline

  • NGS - Single-cell RNA-Seq Analysis

    Bern, 28-29 November 2019

    In room Nr. 304, 3 OG Ost, Universit├Ąt Bern, Hochschulstrasse 4.

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact training@sib.swiss.

    • Schedule

      Schedule

      First day

      Introduction to scRNAseq:

      • Technologies
      • Experimental design

      Quality control

      • Dropouts - Doublets
      • Ribosomal / mitcochondrial RNAs

      Normalization and scalability

      • Feature selection
      • Log scaling
      • confounding factors removal

      Second day

      Dimentionality reduction and cell type clustering 

      • PCA
      • tSNE
      • UMAP
      • Clustering methods (Hierarchical, K-means and Graph-based)

      Differential expression analysis

      • Methods overview
      • DE between clusters 
      • DE between samples (involving data-integration)

      Cell type identification

      • Methods and applications

      Pseudotime analysis

      • Methods and applications