Veronique Miron: Fire mice

Done

• Only import the WT and KO (not the HET)

• The first cell and gene quality control

• Normalisation by deconvolution

• Feature selection and dimensional reduction

• Batch correction

• Clustering at different resolutions

• First rough annotation

• Subset the Oligodendrocytes:

  • Stricter cell and gene QC

  • feature selection

  • batch correction

  • dimensional reduction

• Clustering the oligos

• Interactive Shinyapp with only Oligos

• Differential gene expression between WT and KO for BAMs and Oligos

  • Not enough BAMs
  • All oligos (edgeR)
  • All oligos (MAST)
  • For each cluster

• Differential abundance of cells between between WT and KO in the different oligo clusters, including differential expression between clusters. DA_WT_KO

To Do/ In progress:

• Clean up and analyse the rest of the dataset (cluster QC etc) -> skip, come back to the HETs data