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Dates: 22-25.05.2023

To Decide

• dataset - 1 or 2? 10X ideally
  • 10x PBMC ‘default’ and ‘small’ (both bundled with Seurat)
  • Integration (ATAC, Spatial, etc)
    • See: SingleCellMultiModal, this package has several vignettes, each dedicated to a different dataset
    • Another one: WeberDivechaLCdata

Outline

Day1 - Adrian

• Import data
  • Read10X
• Basic QC
  • iSEE
• Normalization
• Clustering + cluster QC

Day2 - Katarzyna

• Embedding
• Integration (batch effects correction)
  • Harmony, kBET
  • sctransform

Day3

• Cell annotation
  • See this
• Differential Expression
  • Use some rather high threshold to speed-up https://www.singlecellcourse.org/scrna-seq-dataset-integration.html

Day4

• Pseudotime and trajectory analysis

Left out?

• Spatial transcriptomics
• Velocity