Data preparation

  • Download data
  • Convert gene ID to Symbol format
  • Meta data information

PCA & TSNE plot

  • Create DEG object
  • Processing
  • PCA plots
  • TSNE plots

Differentially Expressed Genes (DEG) analysis

  • DEGs: Tumor vs Normal Tissue
  • Create DEG list
  • Volcanoplots
  • DEG table

GSEA

  • GSEA with HALLMARK pathways
    • NES plot
    • Info table
  • GSEA with KEGG pathways
    • NES plot
    • Info table

ssGSEA

  • HALLMARK pathways
  • KEGG pathways