Introdution

Objectives : In this pratical session, you will learn :

  • how to clean single cells data and extract high quality cells
  • identify sub-populations of cells

We will be using the R package Seurat and apply it functionalities to subset the data published in (Karaiskos et al. 2017) (replicate n°3).

Sources of inspiration

This course material is largely inspired by two great sources that we advise you to read/use in details:

  • sincellTE 2020 : MA Dillies, A. Rausell, M Deloger, N. Servant, M. Thomas-Chollier, A. Paquet, cours6_TP_EDA_Normalization_2020.html
  • Vignette Seurat

References

Karaiskos, Nikos, Philipp Wahle, Jonathan Alles, Anastasiya Boltengagen, Salah Ayoub, Claudia Kipar, Christine Kocks, Nikolaus Rajewsky, and Robert P. Zinzen. 2017. “TheDrosophilaembryo at Single-Cell Transcriptome Resolution.” Science 358 (6360): 194–99. https://doi.org/10.1126/science.aan3235.