We are reaching out a challenging task of the analysis (and a very exciting one !).

What types of cells did we capture in the analysis ? Do we identify the expected cell types and can we distinguish different sub-population ? Do we identify “novel”, “surprising” cell types ?

The aim of this session is to understand the different methods that will help you to explore the biological cell types captured by your dataset.

Overview of the scRNAseq pipeline

At this step of the analysis, we have :

  • a gene expression matrix : for each cell, gene expression is available

  • a reduced space : gene expression matrix is summarized in N dimensions

  • a clustering : each cell belongs to a specific cluster

  • a 2D space : cells can be visualized on a 2D representation