single cell rnaseq analysis

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This material is linked to a face-to-face training. It is not intended to be used as e-learning only since it does not contain all the info.

Tools

You need a recent installation of R, RStudio and RTools, together with the following packages:

  • Seurat
  • scater (install via BiocManager::install(‘scater’))
  • ggvenn
  • ggpubr
  • devtools

Data

On the first day we use the data set from Antunes et al., 2021. The data can be downloaded from the brain immune atlas. We use the fourth mouse sample (KO and WT) labeled as Mouse GBM citeSeq. Download the Gene-cell count matrix.

On the second day you bring your own data in the form of a count matrix or a Seurat object (or both).
We cannot process bcl files. Contact us if you have issues obtaining a count matrix.

Slides

  • Slides of the introduction, given by Niels
  • Slides of the introduction, given by Irina
  • Slides for the basic R script

Scripts and R objects

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