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Katarzyna Sikora edited this page Mar 17, 2023 · 27 revisions

Dates: 22-25.05.2023

Outline

Day1 - Adrian

  • Sequencing Protocols
  • Import data
    • Read10X
  • Basic QC
    • iSEE and/ or scCustomize
    • shiny brushedplot
  • Normalization
  • Clustering + cluster QC

Day2 - Adrian

  • Embedding
  • Enrichment (w/ PCA)
  • DE (w/ DESeq2 + MAST)
    • Differential Expression
    • Use some rather high threshold to speed-up; this
  • Enrichment (w/ DE)

Day3 - Katarzyna

  • Integration (batch effects correction)
    • Harmony, kBET
  • SCTransform + Integration + DGE

Day4 - Katarzyna

  • Cell annotation
  • Pseudotime and trajectory analysis

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